I suggest you post a picture of your wiring, it really sounds like a mis-wire.
I've bought a ps2 wireless controller, and the wiring harness from Lynxmotion, and am in the preliminary stages of hooking it up to my autonomous rover. When the receiver is wired in however, it draws so much current that the atom turns off and the light on the bot board dims right out. I've checked and it is wired correctly. I went out and traded in the controller (it was an intec) for a madcatz, and same problem. There's a 6v 1800mah battery on the bot board, just been recharged (first thing I tried) and the pins are set so that 5V go to the controller. Anything obvious I'm missing? I'm going to try to wire it up to the pins near the buzzer instead of pins 12-15 (the ones on the end of the board, as in the ps2 rover tutorial) Thanks for the help!