Factory Anti Theft possibly causing electrical drain

[1BadSnakeBite]

Well, since I bought my Cobra back I have been having problems with it draining the battery while it sits for a few days. I have narrowed it down to the circuit that controls the dome light, trunk light, hood light etc. I found the problem by putting a test light between my neg. cable and the neg. on the battery. The test light started flashing and I could here something in the trunk clicking on and off so I pulled the left side panel and found out that the factory anti theft is making this noise. Everything else seems to be ok as far as wiring. I removed the stereo I installed just incase but it is not the problem. Plus me being an MECP certified installer with my own part time shop, I was hoping I did not make a simple mistake. Has anyone ever experienced the factory Anti Theft causing problems? I am open for suggestions. I want to get this nightmare fixed so I can get on with my other mods.