Hi there, I'm also seeing this bug with evince, gimp and amule.
The recommendation (on https://bugs.launchpad.net/ubuntu/+source/unclutter/+bug/385034) that unclutter be run with -noevents, stops the blinking and cpu usage, but also stops fvwm from cycling through windows with Alt-Tab. The attached patch solves the problem satisfactorily for me, but, not being an X programmer, i don't really understand what FocusOut is for. The patch is against unclutter-8 (from http://ftp.de.debian.org/debian/pool/main/u/unclutter/unclutter_8.orig.tar.gz) bye TAO.
--- unclutter/unclutter.c 1994-04-12 01:40:47.000000000 +1000
+++ unclutter.patched/unclutter.c 2010-06-30 21:23:45.000000000 +1000
@@ -334,7 +334,9 @@
do{
XNextEvent(display,&event);
}while(event.type!=LeaveNotify &&
- event.type!=FocusOut &&
+ /* Some gtk applications seem not to like this:
+ * event.type!=FocusOut &&
+ */
event.type!=UnmapNotify &&
event.type!=ConfigureNotify &&
event.type!=CirculateNotify &&
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