Backups.. And Sync?

Okay this is just a speculation but is it possible that flashing my drive, Or perhaps playing backups can fool around with the sync? xD

Heres what happpens.

My 360 is already flashed. and i love it, When i play original discs on it, i never get this problem, but when i play a back (No matter WHAT game it is) When im playing my wireless controller will just shut off and i gewt "Please Reconnect Controller" this happens maybe once every 10 minutes, sometimes even more often. I can play for hrs with an original game and never get this problem, so im assuming it has somthing to do with the backups? Anyone else experience this problem?


-PS: Its not the batteries . I swapped them 100 times! xD.