I assume you are checking the batteries by measuring voltage. If so, one of the batteries is faulty or the connection is bad.
Forget the copter. If you just connect two batteries together one will charge the other unless they have equal voltage. With the copter, this remains true unless there is something wrong. One possibility is a poor connection to one of the batteries (the one you find to have the higher voltage after flight). The other possibility is a damaged battery, likely with very high internal resistance. A final thing to check is that the current demand of the copter is not exceeding what the batteries can provide.
If both batteries appear to be fine (no puffing or swelling, not hot to the touch after flight, accept charge equally) then I would check the Y-harness and the plugs connecting the harness to each battery.