We have the jailbreak chip and have updated from firmware version 3.40 to 3.41 on the PS3, when we jailbreak the ps3 the green light comes on and everything works fine, even the games load, the problem is the controller, we're using the sixaxis controllers but the buttons don't work when we load the game (if we load an original game from the console via the backup manager) that works fine but neither internal hd or external hd games seem to work with the controller)
we tried one of the move games and it works fine, it's just the controllers for ice age 3 and racket sports via the backup manager, no controller buttons seem to work.
i have searched the net like crazy no one else seems to have this issue that i can find lol
Reset controller from back (There is a little hole)
Resync controller with PS3. (In PS3 settings)
Enter recovery menu and do follows: Restore File System and Rebuild Database.
Maybe is problem with game (I would check that thing first!! - Recopy game on HDD or try with other games)
Or if nothing helps you maybe need the new controller.