Using gnome-light-2.12.0, xchat-2.6.1 and rdesktop-1.4.1. With rdekstop on 1 desktop and xchat set to appear on all desktops, starting on the desktop with rdesktop and having it overlap xchat, switching to another desktop causes xchat to display the dekstop on the portion where rdesktop was overlapping xchat.
Please, report this upstream unless it's a Gentoo-specific issue. http://sourceforge.net/tracker/?func=add&group_id=239&atid=100239