The reason that I asked you to post links was that my XBee shield has a switch that lets me choose hardware serial connection or software serial connection. I slide the switch to software connection while uploading. It fails in the hardware position, just as you were experiencing.
I wanted to look at the shield, and see if there were similar issues/possibilities with your shield. But, it seems as though you found a solution that works for you.
The problem, though, is not the XBee. It is the shield design. The XBee is doing exactly what it is designed to do. The shield is asking it to do things that interfere with what the Arduino and IDE are trying to accomplish.