I have encountered this on rare occasions playing. Xboard enters some mode, apparently expecting some odd input, and I can't do anything. Even File|New Game doesn't exit this mode. It seems to happen when I drag pieces off the board then release, but not always. It's made me lose every time it happens.
Lately, I've been using edit position, and now I regularly experience the same problem. It's really irritating as I get a position mostly set up, then bam, it hits and I have to restart and begin again. Below is an example image. I think I was dragging off the upper left rook off when it hit. You can see a small matrix in the a8 square. This happens every time, and always on a8. The line into square a7, happened when I was trying random ways to exit, clicking the mouse, trying to drag, etc. Perhaps you can tell me what's happening, as the status text doesn't indicate any special mode. ESC and other obvious ways to exit are not effective.