I would strongly suggest that if at all possible you install a fresh copy of windows 2003 on a different server and use the "upgrade (migrate) from older server" options when installing LMS 2.5 on the 2003 server. This will give you the cleanest and most reliable result.
If that is impossible, I would suggest having Ciscoworks make a backup of itself, then rebooting the server in safe mode and manually coping the entire CSCOpx directory to another place on the hard drive. (Leave a copy of the CSCOpx dir where it is as well) I would then try the upgrade to 2003, and then begin the LMS 2.5 upgrade per the upgrade instructions that come in the bundle. Alternatively, you could try setting all of the Ciscoworks services to "manual" before upgrading to 2003, that should keep them from trying to launch after the OS upgrade and having potential conflicts with the OS itself.
