Download and install the Mac OS X Server v10.6.3 Update. This update should resolve the issues in which updates are not downloaded completely, or the update status is incomplete.
Mac OS X Server v10.6: Software updates not visible to clients if they aren't completely downloaded
With Mac OS X Server v10.6 through v10.6.2, the Software Update service will not enable software updates that aren't completely downloaded, or updates where the stored status of the update is incomplete. This issue can be caused by an interrupted download or if there are communications issues between the local network and the Apple Software Update servers.
Server Admin shows an exclamation point next to the update and the update cannot be enabled via Server Admin.
You may see messages such as the following in the /var/log/swupd/swupd_syncd_log:
(time stamp) suserver.example.com swupd_syncd <Warning>: ignored invalid download request for product zzz061-4047, current state = PleaseMirror