I was installing Sharepoint Portal Server 2003 at a client site this week. During and after the install we were getting very strange errors, eventually leaving the site useless until we could figure them out. Installing WSS Service Pack 2 and SPS Service Pack 2 helped get through the installation, but even after the site was completely installed, we still received lots of errors.
It turns out that IIS didn't have script maps for ASP.NET 1.1, so only 2.0 showed up in the list. Though the updates are supposed to work with 2.0, my experience tells me otherwise. Sharepoint Portal Server 2003 *definitely* has issues if you run it in 2.0. To add the option for 1.1 in IIS, you can run:
c:\windows\Microsoft .NET\Framework\v1.1433\aspnet_regiis -i
This will reinstall the script maps for that version into IIS. I changed the SPS site to use 1.1, but I still received errors.
A reinstall put the site back on 2.0, which was quite odd... I got the same errors as before. Finally, to fix it I
disabled 2.0 in IIS 6.0's Web Service Extensions section. Then I reinstalled SPS, which was then forced to use 1.1. All was well with the world after that...