A lot of the new motor controllers have a over voltage sensor built in. If you over charge the batteries the system maybe be seeing a over voltage error and shutting down to protect itself. Just a thought. I would drain the battery a little just to see if that's the problem.

My system will cut off at 56v. A full charge is 54.2v on 4 sla batteries. That is avg voltage for a 48v system. and shuts down the system at 36.6 volts for the low voltage cut off. hope this helps