strange noise from BL36 motor

I just replaced the controller on my BL36 kit (because the screws came lose from the heat sinks and shorted the board on the case) The new controller works (I guess?) But now there is a chattering sound coming from the hub motor. its the same shuttering/chattering that it used to make if I didn't get rolling a little first,like from a dead stop. but now it does it till I'm going about half speed. I have a lifepo4 20Ah battery pack and thought that might be the problem, So I switched it with a set of SLA 12Ah but still have the same problem. Is there some thing that can come lose in the hub that could cause the problem. Or did I fry the hub or the throttle. I rely on my bike as my only form of transportation. Please help me with any feed back or advice.
Thank You