I saw that quite a few people were uninstalling and reinstalling after having problems and I gave it a try too.  It seemed to fix the issues I was having with my controller.  I didn't turn off my antivirus program and it popped up and said that it quarantined a Trojan virus when I ran FSX right after the reinstall.  It looks like a legitimate Trojan attached to the CS777-200 ER GE in FSX so maybe that was the source of my problem.  I don't think it came from Captain Sim, I download a lot of stuff so it could have come from anywhere.