Does it have half width disconnect?  Is the problem exactly 6 and 6?  Just a thought if so that there could be a problem with the disconnect or the drive chain that goes to one side.  If a chain was way too loose it could climb and cause something weird to happen.  Also do all the gears have the same amount of teeth?  I know you said it was new, but those are the simple things to eliminate that I can think of.