It's an under voltage issue with your lipo- the total voltage is lower than what the charger is expectign to see for 2 cells, so it only thinks one is connected as such. Soem chargers are more sensitive than others/have a lower voltage threshold, so sometimes a cell below say, 3.2v won't register correctly- I get the same issue with my old A123 packs ( they discharge much lower than lipos can ). Just start charging them anyway, then after 15 minutes or stop the charge, then restart it & the charger shoudl detect the correct number of cells, just as you've found out