Very interesting! Thank you for making that video and explaining what you've seen. Does this happen with all the controls in the cockpit, or is it just those two? I've seen YouTubers who use lots of windows in VR with no problem, so I'm sorry that you're one of the unlucky ones.
Unfortunately, I still think this is very unlikely to be anything related to my aircraft, but I want to help you in any way I can. Please keep me updated if you learned anything else. Usually I have some recommend Discord server or forum for people to take their issues to, but this is an usual one. Are there any VR specific communities for MSFS that you might be able to ask?
Just to answer your question, sometimes the animation system can get stuck and not take any inputs, literally if your camera is looking one direction. Sometimes this happens to me while developing, and I have to restart the simulator. You can look directly at the panel, and nothing will work. Look out the side windows, and suddenly all the animations will catch up with any changes you've made. Look back forward, and everything will get stuck again. I don't think that's what you're seeing here, but it's possibly related.