Rebuilding or repairing problematic Leopard Server

We have an Intel Mac mini which we loaded 10.5.0 server on and migrated data from a 10.4.11 G4 Server. Since 10.5.1 we have had problems with this machine not correctly applying updates, namely it hangs on writing package receipt. I found that I was able to apply the 10.5.5 update in the terminal with softwareupdate, but this did not working with 10.5.6. Additionally, I cannot run permissions repair, I get "The underlying task reported failure on exit". The system runs fine, but I obviously want to get these issues resolved. Disk Warrior fixes any issues it finds, but this does not help. This server runs Open Directory, web hosting, email hosting, and has a certificate loaded. Thanks for any ideas