I will take a look, I have several ideas I will layout on my end as well and eliminate. Will keep a record.
Its very odd, I do think that the trackir is seeing your app as a 3d application and once it becomes forefront, for example when I use the app to desensitized for, my lousy flying and I want to lower sensitivity, it does that. But once msfs takes control again the profile does not snap back for trackir. Left and right control is fine, but vertical control is dialed down, just like the joystick.
Thats a wierd correlation no? And programs like Fraps and task manager are seeing your app as using the video card, so it makes sense that trackir would be affected since its tied to the video card.
I will Uninstal your chopper, make sure my community folder is naked blah blah. I was testing msfs since it was a baby.
Make sure nothing is running except your stuff. Reboot, cause a power outage to make sure my computer really was off lol. And get back to you tomorrow