3.14v per cell is very low. Depending on the charger, it may decide cell count by guessing at the number based on total pack voltage as opposed to how many balance pins it detects voltage on. 3.14v/cell is a total voltage of 18.8v. If the charger is looking for a nominal voltage of 3.7v/cell on a lipo pack then it is going to see 18.8v as 5.09cells and likely is thinking it is a 5 cell pack instead of six. IF you don't already you may want to try hooking up the balance lead first to the charger to see if that will force it to use that circuit for cell number detection, instead of the main charge lead.
And again, I would not run the pack down that low. Running it that low means you were likley drawing aroudn 2.9v under load, which is enough to damage the cells. If you aim for 3.5-3.7v idle voltage after use that will mean you can be running it hard to the end of the flight without being in danger of hitting low voltage cutoffs or damaging the cells and that voltage level should put you in that 70ish% total discharge range, which is recommended for maintaining battery life.