I've been having this problem too. Happened a couple of weeks ago and I ended up running the auto file repair feature. Thought I'd fixed it, but this evening when I'd switched to the AV-8D immediately after flying the AH64D, I noticed that whenever I tried to adjust the AV-8's controller settings, it automatically selected the AH-64D Pilot control profile every time.
I'm not sure if it only does it if you switch to another module after flying the AH-64D, but it is annoying and can really mess with your control settings if you don't notice in time. I shall need to do more testing to work out when it happens, but I hope this gets picked up on.