Pretend that Zone Master is turned off or all PARTs do not have the PART Zone transmit switch turned on. This is a fairly standard configuration.

If you, under these conditions, have 4 PARTs active: PART1, PART2, PART3, PART4 then you will see 4 MIDI note-on messages for every single piano key press and 4 MIDI note-off messages for every single piano key release. This is because Multi-Channel means that every PART that is triggered will send MIDI messages to its corresponding MIDI port - and assuming you have not changed these MIDI channels (using Zones) - the MIDI channel corresponds to the PART number (1-8). I say 1-8 because these are the only PARTs which can have keyboard control turned ON - meaning the local keyboard can engage the PART.

It is not usual for the notes to be different - usually only the channels would be different. There are ways to setup a PART to output different notes - this is not a typical setup. And the core of your question is more about what to do about the repeated notes. if notes are different values (C2 on MIDI Channel 1 at same time as an E4 on MIDI Channel 2, etc) - I'm not going to run through those traps.

If you wanted to only transmit on a single channel and still keep multiple transmit MIDI channels, then go to the [PERFORMANCE] (HOME) screen and turn off Keyboard Control (Kbd Ctrl) for every PART 1-8. Now any single PART you want to play and have only one set of notes, you would select that PART by touching the PART (1-8) to select. Only that one PART will sound and send MIDI data. The MIDI channel will match the PART number assuming you have not change the transmit channel using Zones.

Single Channel mode will work too in order to remove the "duplicate notes" as all PARTs will only transmit on a single channel with one set of notes. I understand that seems to cause other issues for you - I am only addressing the duplicate notes. For single channel mode, you select a MIDI receive/transmit channel. This needs to match the same channel any external devices are set to (MIDI devices or DAW) in order properly target Montage. I'm not sure of the nature of your issue in this mode, so there's not much more I can relay.

So my question is- is there anything I can do to prevent the stacked MIDI notes while staying in Multi mode?

No. If you have a four Part Performance (3-MONTAGE; 1-EXT SYNTH) then you are going to be transmitting on four MIDI Channels simultaneously. Each Part has uses the entire bandwidth of its own MIDI channel.

What you can do is setup your DAW to properly record what you are transmitting. So here first we will explain what you are actually transmitting; this will be followed by the best method to capture what you are transmitting.

What you are Transmitting
“MIDI I/O Mode = Multi” literally translates to both MIDI In and Out is handled on Multiple MIDI Channels.... This allows each Part to generate its own data. Because a Part can be triggered by you directly striking the keyboard on some channels, while other channels might be triggered by one of the available Arpeggiators.

You do not provide information as to what instruments are assigned to the Parts but it is not unusual, necessarily, that there may be different notes than what you triggered, the Arpeggiator can analyze what you play and block your direct key presses, while it outputs a stored musical phrase instead. An Arp phrase could be chord intelligent, or it could be a Drum groove. Please be aware there will a different configuration necessary for when recording direct key presses (you playing) and for when recording the output of an Arpeggio (“playing”).

_If one of the Parts is a guitar with Arp, it might be strumming chords in response to the chords you voice on the keyboard; you might hold a single key, but what the Arp Outputs is an elaborate strumming chord phrase. To the external device (Cubase) do you want it to document what you played or do you want it to document the strumming... it’s going to have to be either/or.
_If one of the Parts is a Drum Kit with Arp, it might be playing completely different notes than the ones you triggered; again do you want to record the one note you touched to start the drum phrase or do you want to record the stream of events that is the drum groove?
_A problem can arise when the player ‘thinks’ they are actually playing the guitar and/or the drums... if Arps are involved, your key presses are used to construct the musical phrase in the case of the guitar, and your first key press triggers the start of the fixed note drum pattern.

You can understand why each Part would need its own MIDI channel.
Even if you are not using the Arpeggiators, you can understand that Part 1 is on channel 1, Part 2 is on channel 2, Part 3 is on channel 4, and Part 4 is on channel 4. That’s the definition MIDI I/O = Multi. You output on separate channels so you playback databon separate channels.

Now, unfortunately you don’t mention what version of Cubase you are using... therefore we will have to assume you are using Cubase AI (and not Cubase Pro). If you are using Cubase Pro let us know, as obviously on the Pro version you have more elegant solutions.)

Best Practices: How to proceed
On the other versions of Cubase, you will need to setup a single MIDI TRACK. (WARNING: a common newbie mistake would be to create four MIDI tracks and attempt to record - this would be disastrous, because each MIDI Track records all incoming MIDI data). So you’ll wind up with all four channels of information on each of the four Tracks. This is because a Cubase MIDI Track records all incoming MIDI events... each track, re-channelizes the data - it forces all the data back Out on a single channel. So you wind up with four channels of information routed back to your gear four times. Ouch! Please don’t do that!

What you want do to avoid this, is recognize what happens when the Event is generated, say you play middle C, on beat 1, Measure 1.... the event itself includes the Channel number, the note number, and the velocity... for example, in hexadecimal, the event “90 3C 64” translates to:
90 = 9 is a Note On, the 0 is channel 1
3C = the MIDI Note number 60 corresponds to middle “C”
64 = the velocity of 100

By pressing the single Note-on event (middle “C”) on a four Part MONTAGE Performance you generate the following four messages:
90 3C 64
91 3C 64
92 3C 64
93 3C 64

That’s your four events. The top one could be a piano, the second could trigger a string sound, the third could trigger a brass sound and the four could be routed Out via MIDI to an external synth.

You only need a single MIDI Track to record all this data. In fact, it is highly recommended that you only use one Track to record your performing. Each track you open will record all four events. And not only that, each will then force all four events back Out on a single channel.

The Midi Out is Set to rechannelize the data going back to the synths.

Therefore, create just one MIDI TRACK in Cubase, set the MIDI CH Out = “Any”, literally “any”

“Any” means that any channel coming in will be echoed back Out on the channel it came in on. (That is what you want).

Create and arm one MIDI TRACK
Set the MIDI OUT = Any
Record your Multi Part Performance.

When you have completed recording, each note-on, will be documented on its original channel number. 16 MIDI channels can coexist on a single MIDI track without interfering with other channel’s data. Each channel remains discreet.

You only need to separate MIDI data on to separate TRACKS because it’s more convenient to view and edit data when it is on its own visual lane. There is no leakage of MIDI data between channels -the data remains discreet.
You separate the single track’s data by highlighting the track data > select MIDI on the menu bar > DISSOLVE PARTS > “by channel”

This will write out each channels data on a separate MIDI track. By using this DISSOLVE PART *after* your initial recording... gives four Tracks each with its own channel’s data... (much better than four Tracks with all four channels data).

If you have Cubase Pro, you can have Cubase separate the Channel data on the way into to Cubase.
If you do not have Cubase Pro, your Workflow is to record MIDI data to a SINGLE MIDI Track, and after recording use DISSOLVE PART to divide the data to separate Track.

Let us know.

HI Jason and Bad Mister, thanks for replying.
Ok, some more info: I'm using Cubase Pro and I am using 4 separate MIDI tracks as this is the way I always have worked- 1 MIDI channel per part.
So, I have the channels set as follows- MIDI tracks (channels) 1 to 3 have MIDI in & out set to Montage 1 port. Local is turned off on Montage. After recording my arps as MIDI data, I switched off the arp control so the track would play back the sound as recorded which worked great for the 3 parts.
The 4th sound is from an external synth being triggered by Montage on channel 4. The MIDI track MIDI in is set Montage port 1 and MIDI out is set to Montage port 3 to trigger the external synth on channel 4 which works without issue.
Then, when I record the MIDI data for the external synth sound, it works as well. By chance, when moving a MIDI note inside MIDI track 4 (external synth) I discovered that under each note were 2 or 3 (can't remember right now-may have been 3) identical notes. I made sure as I was recording, that no additional MIDI data was being recorded to the previously recorded MIDI tracks from the first 3 parts by watching the MIDI level meters and making sure they weren't receiving data as I recorded the MIDI notes for the external synth sound.
Regardless of what I have to do to record the synth part (I could use an external sequencer or instance, but I wanted to try using the Montage for continuity's sake), There is no way I am changing or re-recording the parts I have finished so far-even if they too are stacked with multiple MIDI notes. I haven't checked the other MIDI tracks to be honest and I need a day to let my ears rest before I get back to the track-and then I will check. Hopefully, if I do have to thin out MIDI data, it won't affect the vibe I've create so far. I will tread lightly, believe me and I've already made 7 backups on separate drives so if I do mess it up, I won't lose my work completely.
Anyway, I hope I've provided enough info to help you better assess the problem. Thanks for your help in this. The more I use Montage with Cubase the more I realize what a fantastic tool it is to help make songs:).

Ok, some more info: I'm using Cubase Pro and I am using 4 separate MIDI tracks as this is the way I always have worked- 1 MIDI channel per part.

Well, as you’ve discovered the way you “always have worked” is no longer successful. What you’ll need to add to your workflow for future Projects is the use of the INPUT TRANSFORMER. Yamaha has built a Recording Template that allows you to continue working as you always have worked. It simply adds the INPUT TRANSFORMER to each MIDI Track to restrict what data is recorded. (We added how to fix your incorrectly recorded data as well... read on...)

If you have been transmitting to Cubase on multiple MIDI Channels simultaneously, previously, then it undoubtedly would have been already a part of your workflow. If not, you need to add it... here’s how:

If you are using Cubase Pro.... proceed as follows:
In Cubase Pro, go to FILE > NEW PROJECT > RECORDING select the Template “Yamaha MONTAGE multi channel recording”

This TEMPLATE makes use of the Cubase Pro's INPUT TRANSFORMER - a device through which your MIDI data will be sorted and filtered.

In Cubase Pro, the INPUT TRANSFORMER is used to create a situation where each MIDI Track can only record the data as specified: the "Sysex Track", for example, has the Input Transformer that Filters all but System Exclusive messages. Each of the numbered MIDI Tracks, 01-16, is set to reject all but a single MIDI channel and to reject Sysex:

You need to setup using this template. Set five MIDI Track into Record Ready:
Sysex
MIDI 01
MIDI 02
MIDI 03
MIDI 04

Please see and follow this tutorial for in depth details: because you’ll want make sure Sysex is not filtered, you want to also make sure you select the appropriate corresponding QUICK SETUP in the MONTAGE: [UTILITY] > “Settings” > “Quick Setup”
And that your Super Knob CC, and Scene CC settings are set to OFF.

MONTAGE and Cubase Pro

This allows a single MIDI Channel of data to arrive at each Track. Let us know.

What to do with your incorrectly recorded data
As to fixing you data (already recorded) if you understand what is going on then you need to simply separate the data.
Any one Track contains all the MIDI DATA (you’ve recorded all four Parts four times; each track contains a complete set of all four channel’s data)
Mute all but one Track...
Set that one Track to MIDI OUT = Any
This will allow that one Track to playback all four Parts as I’ve explained in detail above posts.
After you’ve convinced yourself that what I’m saying is true, you can delete the other copies.
Now execute the MIDI function “DISSOLVE PARTS” by channel on the one Track you kept.

The result will be a Track for each channel’s data.
In the future when recording Multiple MIDI streams be sure you use the INPUT TRANSFORMERs.

Hi BM, actually, each MIDI track has it's own data. Since I edit the notes by hand after recording to fix timing mistakes/change the rhythm etc. I can see the MIDI notes clearly and each track has it's own data. Each track may have quadrupled data but the notes and patterns are unique to each track channel. I'll check it tomorrow and report back.
I am using a separate audio interface so the templates in Cubase would only confuse things for me. I will read up about the input transformer function from the link you provided. I will probably use the audio interface in the Montage at some point but right now I am using the main L&R outputs of the Montage connected to my a.i. and monitoring the audio through Cubase. When it's its time to track or render a mix, then I might need the Montage digital inputs, but not right now. Using multi-channel template might be overkill. Anyway, I'm gonna read that info from the link. Thanks again and I'll report back tomorrow.