Everything is working as it should, except maybe your understanding of the “Mute” and the new KBD CTRL function. It’s often hard to see what someone else is missing, but here goes...

If you manually Mute a Part it will remain Muted until you manually unMute it. If you turn Off a light switch it will remain off until you turn it back On.

Also knowing which Part is currently *selected* is always very important. You cannot manually Mute a Part in the touch screen without selecting it (so that could be part of the issue).

In order to play your KBD CTRL linked Parts, you must be in a Common area (HOME with the cursor highlighting the Performance Name) or you must have *selected* one of the KBD CTRL “linked” Parts.

While on Scene 4, I decided to just play the string part so I went ahead and muted part 1 (piano) and part 3 (pads) via the touchscreen.

These are temporary and not stored. So these mutes are “live”, they are not apart of any stored Scene (yet). If it is your intention to make these a permanent part of Scene 4 you need to update Scene 4... but sounds like you just decided to mute them temporarily... same as if you decided to just increase the reverb or change the volume— it’s live. Do you want these to be apart of Scene 4 permanently?

If not, then they will persist (remain live) until you unMute them. (Or they receive a command to unMute).

Then, next part is to play just piano. so, I went and pushed the button for Scene 1.

And that is where you made your mistake.
You didn’t reactivate (undo) the Mutes... they are still “live”. You have to undo them manually.

Extra Credit:
Please understand that KBD CTRL works in not cutting off the sound because it is a function of the Keyboard Transmitting. You can change which channels and therefore, to which Parts your Keyboard is in touch. Once a Note-On event triggers the Tone Generator, changing the keyboard transmit channel does not stop the sounding Note-On event. The Tone Generator continues sounding.

However, when you Mute a channel, you are stopping its audio from reaching the Output. Totally different. Like turning off a light switch, you are in the dark. And the Mute manually activated will “persist” (remain in effect). You recalled a Scene, that calls for the Keyboard to Transmit to Part 1, and we are sure it is transmitting to Part 1, but you are still preventing the sound of that Part from reaching the output.

If you manually activate a Mute, expect to manually have to unMute it. It has to do with signal reaching the speaker.
Add to this, when you manually touch “Mute” in the screen, you have *selected* that channel...

If you store the Mute status as a function in a Scene (Mixing 2), then you can anticipate its behavior will Mute and unMute as stored and recalled by the Scene Settings. But that is not what you did, you manually edited Scene 4 by muting two Parts... that activity is live and persists until you unMute them in Scene 4.

To store MUTES as part of the Scene you must activate the Scene Memory Switch for “Mixing” — Mute is found in “Mixing 2”.
Stored conditions are recalled when the Scene is recalled. If the “Mixing” Memory Switch is not active in a Scene, it will inherit the current status (the last condition).

It is not a bug. You maybe new to this type of automation, but work with it a bit and it will start to become clear.

@ Bad Mister I just found this comment today, and it really helped me understand the theory behind what's happening here. I can now use a separate MIDI controller (Mektar IMPACT GX61) to control a single part, and play all the other parts with the MODX. For others trying to do this, The separate part is on Part 5. The MIDI out on the controller has to also be set to Ch5, and the MODX need to be in Single MIDI I/O mode (Cog > Settings > Advanced). Finally, all parts to be played on the MODX need to have the Keyboard Control set to On, and the part to be played by the controller set to Off. Then press the little image of a house to deselect the individual part.

Also knowing which Part is currently *selected* is always very important. You cannot manually Mute a Part in the touch screen without selecting it (so that could be part of the issue).

That was key. Thanks, Bad Mister.

In a way I am glad I made this mistake as it taught me to never forget the "focus" of the cursor (to) therefore understand the context I am in. I did not realize it (part) got selected.

Studying how selected PARTs differ from non-selected PARTs will demonstrate an array of concepts.

... what happens differently if the selected part happens to have keyboard control off (nothing "different" happens if keyboard control happens to be ON - with respect to how the local keys control which PARTs send to the tone generator. If Keyboard Control is OFF for the selected PART then there is a difference).
... what happens to the sliders and the "mode" of those
... what happens to the assignable knobs and the "mode" of those (either when [ASSIGN] is lit or not lit - which presents its own set of knob personalities)
... how visual indicators can help you identify the current mode (how LEDs change and where to look)