Are you using external hardware to tune nav/com frequencies? If so, check your bindings, or perhaps disconnect that hardware as a test to see if the issue persists.
I had an issue once that occured whenever I had brought up ATC via a button on my Streamdeck. The three key sequence I was using was working fine, but for some reason it was also being picked up as a non-modified key, and it causes by VS to increase by 100ft with every press. I knew it was happening, but it took me a few hours to work out what I was doing that caused it. I simply unbound the keyboard command to increment VS.