R1Pro Cogging?

[gtxracer]

I just got all my stuff together for my CRT build. Here's the specs:

CRTx1
9XL with RCM heatsink
R1Pro with two 35V 1200uf caps
CCBEC
Neu 5s 5000mah pack
JR 9000T
Losi Sport synthesized Rx and Tx (for now)

I had a slight mishap when I first plugged in the setup for a test run. The little spring on the deans plug bent towards the other side (polarity) and sparks flew. It fused the deans together but since I had the BEC wired in through it's own separate deans connectors I unplugged everything right away. I'm pretty sure the battery is okay. The R1 and Rx are fine, no damage. There is some cogging though. I was thinking it was my Tx batts since they aren't fresh and could use replacement. It caused my setup to eat a spur gear, 46T Kyosho. I only have 2 spares so I would rather not have this happen again. Any tips? Is this normal with low batts or is my BEC causing this? Any help would be greatly appreciated.