you need to check the charging First, and make sure that current was headed through it, and all that stuff is WORKING.
if all that is working, and a current is headed to the battery yet the voltage will not rise THEN, you can assume that the battery is BAD (and dangerous) .
a bad li-ion will not "accept" the charge, and therfore will not raise in voltage.
you need to charge the cells as single units, if you were charging protected in SERIES, one cell could be completed and cut-off, and so the other cell would not get a full charge. or "The series is not balanced".
other ways to see what is going on:
1) discharge it to say 3v , then wait for a while and see that the voltage is stabely low, then put it on the charger Monitoring the voltage , it will go up while on the charger, then see where it quits going up.
2) charge it for a bit, then take it off the charger, and see how badly the voltage sinks when just removed, and removed for a while, a bad battery will visually drop in voltage while your stading there quite often.
3) check a Known to be working cell unit on the same charger, see if the results are similar, if they are then check the charging.
of course the above is completly dangerous, because a battery that will not accept the charge lets the power off as heat, heating the battery internal, a FAST charge under those conditions can even thermally kick the battery into an ignition point.
a slow charge just keeps trying, and trying not accomplishing anything, and the heat building up gettting worse and worse, still not safe, but not likly.
SO
you FIRST have to assume that the battery will BLOW UP
sorry but there is no way around this, it is very unlikly to, but you still have to assume that. Then check the charge. then check the voltage.
another symptom you will often also see, is that the battery self discharges all by itself.
if the li-ion cell is "bad" there is nothing you can do that will "fix" it permentally, there are things that might make it look like its going ok, but the battery is still schmuck and the battery is still dangerous.