This sounds like the same problem that I was having with the Gimp under Afterstep 2.x. According to the developers, this is due to the applications in question abusing USPosition (http://mail.afterstep.org/pipermail/as-users/2005-November/001726.html). The fix is to modify the database to include UseCurrentViewport for all affected applications. E.g. I edited /etc/X11/afterstep/database to include the lines:
Style "gimp" Icon logos/gimp, UseCurrentViewport Style "gimp-2.2" Icon logos/gimp, UseCurrentViewport -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
