Did the controller relay fail "closed" and leave the charger running? I've seen that happen a couple times. If that's the case, you batteries are cooked. I haven't seen anyone bring batteries back to new"ish" after cooking them. There are a lot of methods to try, but you may end up needing new batteries...especially with only a 5 minute run time. Good luck.
Billy
From: Ferguson Apiaries <ferga hay net>
To: "elec-trak cosmos phy tufts edu" <elec-trak cosmos phy tufts edu>
Sent: Wednesday, April 23, 2014 9:59 AM
Subject: (ET) batteries