After a few weeks, a patch has been released a few days ago that fixes the fglrx lag when minimizing, maximizing or opening a window on ubuntu jaunty 9.04. The lag was severe freezing the entire desktop for 1-3 seconds, almost making desktop effects unbearable to use.

For those who would prefer to compile xorg;
http://launchpadlibrarian.net/26424345/107_fedora_dont_backfill_bg_none.patch

PPA is available here;
https://edge.launchpad.net/~ubuntu-x-swat/+archive/xserver-no-backfill

Launchpad link for this bug;
https://bugs.launchpad.net/ubuntu/+source/fglrx-installer/+bug/351186