This is a bug of sorts, it affects both Xboard 4.4.2-1 (Ubuntu repository) and 4.devel~hgm-5 (H.G. Muller web site), each one installed on a different computer. It is not particularly critical, especially because it will be seldom triggered: I've installed pyChess and it messed up with my FICS settings, setting pin on, availinfo on and something else - I don't remember but I believe the problem is related to availinfo anyway, as I when I set it back to off Xboard behaved normally again. What happened when availinfo was on is the board would change size erratically, with two side columns (for captured pieces?) appearing and disappearing, and the board was unresponsive during this, or worst, the wrong piece be moved.
Sorry for the bug report somewhat imprecise, but as I said, this is probably very uncommon, and just setting availinfo to off cured the problem.