It sounds like what's happening is that you're tripping the battery overcurrent protection that is built into the individual lithium cells. Once that happens, the only way to reset the protection is to remove all current draw from the cell, which you can do by pulling off an battery tube endcap.
You can watch all this happen in the telemetry if you're driving the ROV hard. In the telemetry field there are voltage measurements for the two battery packs (I think they're called BatV1 and BatV2, or something like that). Normally each batter pack will read something like 11 volts. But under hard driving conditions, you will occasionally see the voltage on one pack go to zero. At this point you're basically only driving on one of the battery packs, and further hard driving can kill that, too, leaving one with a dead ROV. Until you open up a battery tube, that is.
We have also noted that if you get a leak in a battery tube, it can short out the battery protection circuit and cause a shutdown as well.
At some point we'll probably investigate the characteristics of the battery protection circuit, to see if some fix (maybe adding some capacitance on the battery bus?) would reduce the incidence of nuisance trips. One could try using unprotected cells, but we definitely don't recommend that- the protection circuit is there for a reason. What might end up happening is that we just limit the max throttle of the vehicle to a level that won't ever trip the battery protection circuits. But I would prefer not to do that, as there might be a situation where you actually need that power. Perhaps a better solution is some kind of limit checking on the telemetry values that warns the user that he has popped the overcurrent limit on one of the packs.