Port Isolation is usually the trick…
Do you have the MIDI Input on your MIDI or Instrument tracks set to “All MIDI Inputs”?
If so, change that to your Main Keyboard MIDI controller.
In my case here It’s MIDI port A. Now the track will only get input from my main Performance Setup (several MIDI Keyboards, pedals, and more combined and managed in Bidule and routed to a Virtual Port named “A”).
This way whatever you might be doing on the CC1 won’t bleed into your MIDI tracks.
Also be aware you can toggle specific ports out of the “ALL MIDI Input” soup in “Studio Setup/MIDI Port Setup”:
Notice the column with check boxes for "In ‘All MIDI’.
I.E. If you primarily use the CC1 to remote control Cubase itself, as opposed to sending CCs into your hosted instruments, you might want to take it out of the 'All MIDI Inputs" chain.
I.E. If the device uses Mackie protocol or something similar, you’ll definitely want to take whatever port it does that over out of the “All MIDI Inputs” equation.
I don’t have a Yamaha CC1 to know how many Ports it provides and what all ‘languages’ it can speak, but I’ve seen the problem before when I was using an Akai MPKII. The way it came new out of the box it was a mess, as they had EVERYTHING that shipped with it set up to use the same port, and they also had used CC64 to ‘Mute/Unmute’ Tracks! So you’re playing your piano part, happily workin’ that pedal, and Mute on the channel mixer was steadily pumping on and off! Duuuu…
That particular MIDI controller has two MIDI ports to work with, so I promptly rebuilt a preset for it that takes advantage of both ports.
I isolated things meant to remote control the DAW (Legacy Generic Controller, or the Newer MIDI Remote API) to port 2 and filtered it out of the ‘All MIDI’ chain, and kept things I want to go through to Instrument/MIDI tracks on Port 1.
So, check your CC1 device to see if it offers multiple ports to work with. If it does, take some time to plan out presets for it that isolate things ‘instrument’ to one port, and things ‘DAW’ to another.
In cases where I need to ‘merge’ multiple controllers together so they behave like one…I make use of 3rd party software like Bidule or Bome, and pipe their magic into the DAW via Virtual MIDI ports (loopMIDI here, but I think it’s possible to get native loopback in Windows 11 now with the right tools?). I find it worth the bother, as such utilities can turn really dumb and limited controllers into very smart and flexible ones.
If needed you can still Filter at a Global (Project) level, or on a Track by (Track) Basis.
The P set of transformers can be set one time and applied as needed to individual tracks. Use the T option if it’s a ‘one off’ scheme different from the Global “P” one that should only apply to a single track. AFAIK, there is no limit to the number of different T transformers you can set up and use in a project. Each track can store its own unique transformer there.
If you need more complex filtering or transformation that requires more than 4 steps, you can stack even more on a given MIDI or Instrument track as “MIDI Inserts”.
Again with the old MPKII…they never fixed the firmware for using pedals of either polarity. To fix my ‘backwards pedal’, I kept a global (now called project) transformer on the ready to ‘invert/mirror’ the Pedal events for that thing in real time. Since I needed it on pretty much every track when using that keyboard, I loaded it one time as a P filter (Back in the day it was called a Global transformer, and there was a little toggle style button for it near the top of the track inspector) and simply toggled it on for tracks as needed.
