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If after an update is applied to Mac OS X 10.5.x Server you find yourself unexpectedly looking at Server Assistant upon restart you might try this to get your server backup to normal. At least in my case this problem was solved by doing the following:

Start up in Single User mode by holding down the Command and S keys at boot, then run these commands:

/sbin/mount -uw /
rm /var/db/.SoftwareUpdate*
reboot

You can also delete the problem files by logging into the server via SSH and executing the rm command, provided that you still have SSH turned on of course.

Under some circumstances when a software update fails for any reason under Leopard and Leopard Server it appears to not properly remove the /var/db/.SoftwareUpdateAtLogout and /var/db/.SoftwareUpdateOptions files. If those files are present they can cause Leopard Server to invoke the Server Assistant mode at startup. Force quitting the Server Assistant just causes the Server Assistant to relaunch. Instead boot into single user mode and delete the offending files.

/var/db/.SoftwareUpdateOptions appears to be an XML-formatted .plist with settings for Software Update while /var/db/.SoftwareUpdateAtLogout is just an empty file which if present causes the system to run Software Update and install any pending updates at next logout or restart. Why these files are causing Leopard Server to start up in Server Assistant is beyond me but is almost certainly a bug. There is another file in /var/db called .AppleSetupDone which if missing will cause Mac OS X to run the Setup Assistant/Server Assistant once upon startup, this bug is reminiscent of that ‘feature.’

This fix was inspired by Mark Douma’s post and fix for the same issue happening to Leopard client in the Apple Discussion Forums.