I'd check all your motor connections. This includes the bullet connectors (could be dirty), the bullet solder connections, the battery plug (cold solder joint and/or dirty contacts, and the solder connections where the wires meet the ESC.
If that's not it, you might have weakened/damaged some of the FETs. My setup (3s on the 3300) in the CRT.5 runs prefectly fine with no cogging at all.