Controller having to be reset

[fastturtle]

I'm not sure what causes it, but the bug happens as follows:
Sometimes, I'll be playing and at between menus/game modes, the game will stop recognizing my fightstick as the selected controller, and I'll have to use the keyboard to go to Options to assign the controller again. What I mean by between menus/game modes is for example, I will exit training mode and then have to reassign my controller, or sometimes I'll be searching for ranked matches and when I get one, the controller will stop being assigned (which automatically backs me out of the match before I can even assign my GGPO settings). I do have 2 controllers plugged in aside from my keyboard - they are a regular wired 360 controller and a Madcatz SE Fightstick. I'm not sure if it's this way every time, but right now, as it just happened, the 360 controller (which I'm not using) is Controller 1 and the Fightstick (which I am using) is Controller 2.

Hardware/software info:
Skullgirls(not the beta)
Madcatz SE Fightstick (specifically the WWE Brawlstick)
Official Xbox 360 Wired Controller
Windows 7 (most recent updates/service pack/whatever)

If any more info is needed I'll be happy to help in any way I can.

Thanks!