same ga, same security problem

I've got the imfamous security lock problem it seems like everyone has with their 99-00 ga's. I installed a battery bypass switch in my ga, thinking that if i shut down the computer, the security system won't have a choice but to reset. WRONG. I disconnect the battery when the security light comes on, the security light then goes off, then i reset the bypass switch and the secuirty light is still off. But when i go to start my car the damn light comes back on. But then i can wait 10 minutes and the light will turn off and i can start the car just fine.

Anyone know what the deal is here?