You aren't the only one with this problem in a 99 Bonneville.
I'm going to be putting a different headlight switch in tomorrow and will post back tomorrow night.
I to first experienced this when I installed an Alpine deck last summer. Switching a factory deck back in didn't fix anything -only made it worse. If you put a stock radio back in I bet you'll experience battery draining problems due to a bad power antennae relay -I know, because I did 3 times -on my old 99 SSEi, my old 98 SSE, and my current 99 SSEi.