Welcome to Yamaha Synth...
You don't provide us with too much information about what you are doing with your software. But you can eliminate any delay by monitoring your S90 XS direct. That is, with LOCAL CONTROL set to ON. This will allow your key presses and control movements to travel directly to the synthesizer tone engine without going through the software, to trigger the internal sounds.

We will assume you are using the proper Yamaha USB-MIDI Driver for your particular computer type and operating system. These can be found at the official Yamaha Download site:

http://download.yamaha.com

Select your country
Type in your Model Name > click "Search"
When the Search Results appear, verify by clicking on the model name. "S90 XS"

You can further refine your search by entering your computer operating system - you are looking for the appropriate USB-MIDI Driver. Currently for Windows 7 it would be version 3.1.3 (it comes in 32-bit and 64-bit).

The delay you are experiencing is most likely due to routing signal through your computer. We are not certain what you are doing with your software - we are assuming you are doing notation (if you are doing something different please let us know... Sibelius is not a Yamaha product and I have no experience with it. If you are sequencing with it and require LOCAL CONTROL being OFF, then make sure you have the Yamaha driver properly installed and selected inside your program.

Let us know.

Latency can be horrid on the S90XS if you leave unnessary zones activated but with the volume off and you start playing piano parts that include glissandos or organ palm smears etc.... It will bog down the processor.

This is probably not your problem but shutting OFF unused internal zones is a good tip to emphasize on a S90 forum.

Latency can be horrid on the S90XS if you leave unnessary zones activated but with the volume off and you start playing piano parts that include glissandos or organ palm smears etc.... It will bog down the processor.

This is probably not your problem but shutting OFF unused internal zones is a good tip to emphasize on a S90 forum.

Shutting off all zones would be the good tip, as using multiple transmit channels from the S90 XS must only be done with proper setup in the computer, particularly if the software is echoing signal back to the S90 XS. If the software merges MIDI signal to a single OUT channel, then chaos will most certainly follow!

It should be standard procedure that when working with a notation program (Sibelius) like the original poster mentioned that you not work with Zones (Master mode) at all. There would be no reason or need to do so. The S90 XS/S70 XS will transmit on only one MIDI channel at a time (which is definitely what you want) in Voice, Performance, Multi modes. Zones are defined by the Transmit function and are only found in Master mode. So Zones will never come in to play at all.

Just to clarify: in Master mode you can setup to transmit internally, externally, or both on as many as four MIDI channels simultaneously - one per Zone. Master mode is the only mode where the KEYBED of the S90 XS/S70 XS can transmit on more than one channel at a time. And would not, typically, be used with notation software, at all. If you direct (echo) four MIDI channels of data to the same Part, no doubt, you will run yourself out of polyphony much more quickly than if you operate normally/properly, of that there is no doubt! We wouldn't call that "latency", more of a "log jam".

In most recording software, (talking about DAW software now, like Cubase, etc.), the MIDI INPUT will receive any, literally, "any" incoming MIDI channel. This is because, in MIDI, every channel event includes the MIDI channel number designation. This is how multiple channels of MIDI DATA can coexist on a single track yet remain discreet.

When you set a MIDI Channel in your software you are usually re-Channelizing the data on the way OUT. The channel represents the MIDI OUT from the software. This is how, when you're improperly using Zones with external software -your potential four Zones can get "merged" and play (trigger) one internal Part, once for each Zone that is active (this is a common MIDI routing mistake).

So a Voice that normally used 2 notes of polyphony per Note-on could now demand 8, so you can see via simple math, how you can run yourself out of polyphony if you unknowingly are merging events! There are only like 4 or 5 VOICES that use all 8 Elements simultaneously (one of them is a drawbar organ, "All Bars Perc AF1&2") a bad routing setup could mean each key pressed is like sending a request for 32 notes of polyphony! Ouch! (But this must be classified under "pilot error").

Hope that clarifies what you are describing as horrid latency, it's really just a log jam... likely due to improper routing of signal. And you're right, it should be avoided!