After reading your post carefully I notice that you changed all batteries. My guess would be that a wire was left disconnected from one of the battery posts. A lot of systems add a wiring to run accessories. Just a thought.
Silicone is not compatable with epdm or tpo roofing material. Been in the roofing business a few years and the best I have found is a neoprene bases sealant called NP1. That is what manufactures like fibertite and firestone say you have to use if you...