Flow control should be disabled on QGC, unless you set the Xbees to work with that.
Verification of bidirectional data is done by opening up 2 instances of X-ctu connected to each Xbee and using the terminal windows to send text back and forth between the 2 Xbees.
One should be Coordinator AT and the other one Router AT. I would update to most recent FW on both bees.
Go over all connections, could just be as simple as a cold solder joint somewhere. The intermittent nature of the problem could indicate that 1 of the Xbees or its antenna could have a problem.