The Octane 2 will dead short your packs (zero volts).
If your just discharging the batteries until the lights onthe Octane 2 go out, that could be the problem. If you want to deadshort, you really need to put a wire or solder across the pack. Leaving the pack just deep discharge doesn't seem to have the advantages of actually deadshorting.
Kinda like the Karate Kid "Karate do -yes ok. Karate do- no, ok. But Karate do- maybe *squick* squashed like grape!!"
That being said, I'm sure Kane's Haus of Voltage will get you right back on track.