As far as I understand, you use 2 batteries in series with a buck regulator connected to them, and one battery (on the same position in the mod) discharges even without load. If so, seems that this battery is shorted in any way. Maybe not exactly shorted, but loaded. Try to interchange the same batteries. If always discharges battery only in a certain position, this is the problem of the mod hardware. Check wiring inside the mod. Maybe some glue you used inside the mod is conductive. Or you used a foil inside etc. If you did not modify anything and you are shure that your batteries are healthy (of course after discharge to 0 battery is not healthy), ask developer about your problem, maybe something soldered wrong.
P.S. try to keep your batteries otside the mod and check if their voltage is the same after, say, night. Also observe correct polarity when connect.