I am supporting another consultant who is participating in a migration from SPS2003 to MOSS 2007 (yes, there are still many companies who have SPS2003, larger companies tend to move slower).

So, customer applied SP3 and my friend scanned with prescan.exe, orphans found (as usual) and when she tried to spsadm repairorphans url; the site was no longer online, it wasn't even listed in the portal sites.

We still don't know why in hell the SP3 didn't updated the Content DBs schema, but there was a lesson learned, run the following query against your Content DBs.

SELECT SchemaVersion,BuildVersion from PortalSchemaVersion

This will bring two columns

SchemaVersion (DB Version): If this is 2.0.40.1 you're still in SP2!!!

BuildVersion (SPS Version): If this is 11.0.8126.0 you're still in SP2!!!

Go check those numbers cause something may be in a dangerous state.