It seems that the EPEL rsync script is not running with --delete, meaning that all previous copies of packages are still in the repo, even though they are no longer in the repodata.
Example:
-rw-rw-r-- 1 263 263 22010747 Dec 4 13:40 clamav-0.94.2-1.el5.src.rpm -rw-rw-r-- 1 263 263 21723278 Nov 5 13:46 clamav-0.94.1-1.el5.src.rpm -rw-rw-r-- 1 263 263 20385113 Oct 27 21:58 clamav-0.94-1.el5.src.rpm -rw-rw-r-- 1 263 263 18080416 Jul 14 05:38 clamav-0.93.3-1.el5.src.rpm -rw-rw-r-- 1 263 263 17084530 Jun 18 16:23 clamav-0.93.1-1.el5.src.rpm
the rsync script should remove packages that are no longer in the repodata.
See also: http://www.redhat.com/archives/epel-devel-list/2008-December/msg00015.html
fixed, a left over hidden dir was in the tree without permission to delete. resulting in --delete-after failing to happen. and to speed things up added a --exclude=".snapshot" to the rsync
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