The batt should have been 3.7-3.8v (50-60-65% capacity) when you got it new, they are only partially charged before they're shipped. Part of the prob is that the pack should have been charged before you ran it -that is SOP with lipo - charge it fully before you run a new one. I suspect what you're seeing cell balance wise may be related to running it first rather than charging it first. This cell imbalance and low voltage should go away after a few cycles.

Chargers like yours are pretty accurate usually, dbl check your esc settings and be sure its on lipo and that the lvc is set. I'm not familar with the esc, but if you can set it to 3.2v/cell (6.4v for a 2S) it will provide some safetly cushion. Running lipo to lvc at 3v/cell is tough on them and you won't get the life from them versus not running to lvc everytime or using a higher lvc.

Go ahead and run it again from where it is and then re-charge it and see if charger numbers make better sense. Lipos can be overrated - I've read of 5000mah rated lipos that routinely charge to 6000+mah, so you may have really put 5000mah back in and run the voltage down pretty low.