What is probably happening is your xBee is configured as an end-node and going to sleep. It shouldn’t do that while your communicating with it, but it will go to sleep if you don’t send any traffic to it for awhile. In the perfect world you would never know it is sleeping as the serial traffic will just be buffered for a brief second while it is sleeping and processed when it wakes up. But if your USB to serial device is having communication problems it will appear to lock up. You may want to try turning hardware flow control on in your XCTU “Add radio device” settings. If it is already on turn it off and try different settings.
Once you get it communicating you will need to follow the instructions I laid out in this post FAQ: Mapping your ZigBee network with Digi's XCTU