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Challenge Tower button problems

I've seen a few threads that relate to button mapping problems, but I'm not sure if my problem is exactally the same.
I use my Mad catz TE fightstick (stock, not combat panel) to play and I have it set up like this:
(FP) (BLK) (BP)
(FK) (TAG) (BK)
Now, every so often the game will just set it back to default. It's not due to certain challenges because I've lost one on purpose and when I played it again my buttons were back to the way I set them.
So far I have only had this problem in challenge tower, but if it carries over into other modes, like online or versus, it will cause problems as I'm sure you all know.
Thank you for your time, and hit me up for some games if anyone of you are down. XBL: Po0tY mAcK