Re: Constant Beep From Battery Compartment
is it a lead acid battery? It's possible when you recharged the battery the water was evaporated and some of the plates fused/welded together when they dried out. As the battery continued to charge the rest of the water was boiling due to the short inside the battery and the "beeping" you heard was the steam pressure escaping from battery. There is no speakers or anything under the seat unless you have some kind of after market alarm system.
Either way you need a new battery. I don't think your bike's charging system is messed up.