Lipo chargers won't charge with a lipo that has a voltage reading thats below 3v/cell, so a 4S needs to be at 12v or better. There are inaccuracies in these chargers so its not surprising if you go to 12v on NiMh mode it may not charge yet as a lipo. I try to get teh voltage up to 12. something.
Another tip - 1.0amp on NiMh rate will cause voltage to go up too fast unless the capacity is large. I use 0.5amp - this also gives a more balanced charge to the cells at this lower rate.
The best way to fix low voltage cell issues is with a lipo charger that charges only thru the balance connector. If you're going to use lipos from HobbyKing, next time you see this in stock and are ordering, get one -
http://www.hobbycity.com/hobbycity/s...Charge_Capable
I have one and its already paid for itself. It forces the low voltage cell to come into balance with the others.