Not only my skins but my stick settings seem to be disappearing which really bothers me. I'm not sure why it happens but I've noticed that all of a sudden my plane loses control and my settings get all screwed up. I may just have a conflict of some sort and looking for a fix.
Have you just bought a X52?
If so, I had exactly the same problem. I'd be flying along, in the middle of a fight and then my stick would lose calibration and start pulling down and to to the right. I had to pull out of a bunch of good fights because of it.

The problem is that the X52 isn't getting enough power from your standard in-computer USB port. The good news is that that $30 for a powered USB-hub will entirely solve the problem. I bought one for myself and I haven't had a single calibration issue since I got it.
