I'm using the applet here: http://www.chessgames.com/perl/chessgame?gid=1069669 with gcjappletviewer. (As of this writing I needed a patch to make this work at all, see the classpath-patches list.) When the applet window first comes up, if I move the mouse from the applet window into another unrelated window, the applet window will do a full refresh. If I move the mouse from the applet window to the desktop, nothing special happens. (The same thing happens when moving the mouse from a window into the applet, but again does not happen when moving from the desktop into the applet.) After I make a move in the applet, this refresh behavior stops.
Are you using focus-follows-mouse? If so, this is a known problem; a change in a window's active state causes an expose event on the entire window, which triggers a repaint. We need to find a way to prevent that expose event in the gtk peers.
Yes, I'm using focus-follows-mouse.
Fixed on GNU Classpath mainline.