Does the phone charge normally when you use the stock charger?
I have heard of people using cheap chargers that are rated very low (<500ma) or malfunctioning can cause this issue... a sales person in or office had problems charging his phone a few weeks ago so we asked him to bring in the charger, not sure where he got it but it looked kinda like a factory Motorola charger, but when we looked at it closer it was only rated at 5V@250mA, which he had obviously mixed up chargers for something.
I would fully cycle the battery (under 15% to full) twice with the stock charger and then see if the problems persist under the stock charger, if it clears up suspect the dock or it's P/S, if it still has issues it might be the battery itself.
Might I suggest you get an app called Gsam Battery Meter? It can help you fine tune exactly what is using battery including how much each brightness when it's set to auto is using. It helps find apps that might be stuck running, signal strength battery usage, etc.
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