I ran the SBS Best Practice Analyzer tool and it recommended that I re-install sp1 for SBS2003.
After I rebooted and immediately noticed that companyweb was not working.
I did several searches and found some information here that led me to uninstall and reinstall sharepoint and restore the databases.
I was able to get companyweb back up but I have since noticed that no one can connect to their desktop from RWW and cannot download the connection manager (sbspackage.exe) from the remote website.
If you try to connect to the desktop, it gives the standard "make sure desktop is connected to the sbs network... etc..." and when you try to download the connection manager it takes to a web page cannot be displayed. If you right click the link and save as, it says the server returned an invalid or unrecognized response.
Everything was working before I reapplied the service pack.
This is SBS2003 standard.
OWA works. I can still navigate to the RWW, I just can't connect to any servers or desktops.
Incidentally, I re-ran the SBSBPa again and it said I needed to change the asp.net versions to 1.1.4322. When I did this, the websites were unreachable again. I have them set to 2.0.5072 now.
Any help would be appreciated.
I can provide more detail if needed.