I'm having the same trouble. I have to punch the keyboard hard sometimes to get everything working. Happens more with Amazing and Noir. I've tried 2 different keyboards with the same results. I've also tried reassigning keys but no luck there either. I bought a new mouse and that's working better so I went ahead and ordered a new keyboard since both of the ones I have are kind of old. I'm not sure the trainer has anything to do with it, though. Everything with the trainer is working great. I've run the game with and without the trainer and I get the same results.
My system (yeah, it's getting up there in PC years)
ASUS M3N72-D
AMD Phenom 9600 Quad core
4GB DDR3
NVIDIA GT220 1GB GDDR3
Win 7 x64
if you punched the kb to work hah?
if it doesn't try to kick it!
ha ha ha ha...funy hah?