U may be onto something with the aftermarket anti-theft thing. Think of this, most anti's draw power continuously in order for their sensors to pick up some no-key entrance or fooling around with the ignition, such as that. Now, I don't know exactly where the installer sliced into your wiring, where he placed any sensors, or where he accessed the power supply {but I would bet it is a constant on lead}. Try to "unpower" the thing completely, you have a draw that is weakening your battery, and possibly doing very bad things to the normal electrics of your ride.