Usually you set your cutoff at 6V for a two cell lipo. You can take them down to 2.5 a cell with a hard cut but 3v a cell is safer. Try setting the voltage cut a 6v and monitor the battery and see if it goes into cut. The problem might lie with the way the lipo battery discharges. The voltage curve of a lipo stays pretty flat until you reach a certain voltage and it really falls off fast. Also, update your firmware and see if that fixes the problem. I have had updates that did not fully take using the castlelink in the past.