gtk+-2.0.8, when used with metacity, causes window placement and minimize problems. After about 30 windows have been closed, metacity crashes and window placement will be disrupted. Minimised applications may reappear. Does not happen with gtk+-2.0.6.
http://bugzilla.gnome.org/show_bug.cgi?id=94806 describes the problem. http://www.freebsd.org/cgi/cvsweb.cgi/ports/x11-toolkits/gtk20/files/Attic/patch-gdk_x11_gdkwindow-x11.c?rev=1.1&content-type=text/plain is a patch to solve the problem. Will attach new ebuild shortly.
Created attachment 5903 [details] Portage branch with patch from FreeBSD
gtk+ 2.0.9 is released, in portage and fixes this problem. please try that and if the bug(s) persistm reopen.