Odd. I don't believe the Repair undoes the update. MSI installers are supposed to take the updates into consideration. You should be able to tell by looking at the dates on files in your ..\server\bin folder for example and see 8\5\2009 dates from the update.
I can't say what went wrong, but you might want to stop the service, run a BackupOfflineRepositories, RestoreColdBackupRepositories and then execute a RecoverRepositories from the RepositoryAdmin folder. This should validate the integrity of the Repository and update it's transaction logs which should help speed the startup of the service.
Regards,
Dave