When it says Low voltage, "S" set incorrect. Low cell, get it to individual cell voltage to see which cell is low. What ever cell is low, set charger to NiMh to 1amp. Get that cell upto 3v. Babysit the charger every 30 second turn the charger on and off. Once cell is at 3v, change charging mode to Lipos. Should charge normally. Set up ESC cutoff to 3.4v so this wont happen again you you drain too low. Lipos not to discharge less than 3v.
Read manual to get reading of individual cell voltage.