you can program it with the transmitter or computer. It might be automatically on auto cutoff too. I wouldl go through programming once at least and make sure nothing is too messed up.
I run all my cc controllers at 3.2 and I have yet to have any probs.
1. MBX-6 T8 1900KV, RX8 ON 4S
2. MBX-5T 1520, MMM ON 5S
3. MBX-5 ONROAD CONVERSION 1515, MMM ON 5S
4. MRX-3 ON ROAD CONVERSION 1512, MMM ON 6S
5. TEN T 2650 T8, MMP ON 3S
3.2 is insufficient, this graph is from a 5000mah 30c pack on a MMM, LVC did not cut in at all, the sampling rate of the LVC seems to be too large so it's not very sensitive. I recommend a LVC of 3.5V a cell to prevent a nearly depleted battery dropping below 3v/cell under load.
What battery was being used? Any amp draw data with that run? That battery doesn't seem particularly impressive given the 5000mah/30c specs. The pack hit 3v/cell within 3 minutes! No way that is a 30c continuous pack in real life.
Based on this graph, I would say the battery was insufficient(which then makes the 3.2volt setting insufficient as well).
I just hook my mmm to the computer an it says for a 4 cell lipo cutoff should be 12v . so is that at 3v per cell?
If you are using high end/quality lipos, I think the 3v/cell is fine. The cheapy/lower quality cells usually won't hold voltage as well and likely need a higher number to prevent over discharge as shown in fastbaja's graph.