I'm only now just getting into my battery failsafe levels, it's kinda tricky stuff!
Are you using a digital charger and/or cell checker?
My fancy cell checker also would say "60%" after having complete a flight, which always had me confused, but I've leaned to pretty much just use it as an indication if the battery is charged or not.
the most important is what level the cells are at, what the total voltage is, and then how many mah you are sending back into the battery after a flight. As mentioned, if it's under 1750, you should be ok.
as for cell levels, I've heard it's ideal to never go below 3.5v a cell.
I've recently been changing my battery failsafe levels lower, as I'm flying a rather heavy Phantom and it seemed to want to self-land pretty quick!@.
I changed my levels to 11.3/ .6 / 10.70 for first level protection
and 11.15/.6/10.55 for 2nd level protection.
and noticed a significantly improved flight time while still not sucking out more than 1750mah from the battery.
So I'm rather happy.