I have the same problem, did you manage to solve it?
WIndows vista with IIS 6 support.
Running multiple sites.
Framework 1.1 , 2.0 and 3.5 installed.
Episerver manager and Episerver CMS manager give the same error (have some 4.xx sites installed for the Episerver manager)
I solved the problem, had to reinstall the frameworks.
Im developing in Vista/IIS 7 and had the problem for both the episerver CMS manager and the previous one for Episerver 4.xx
I also had to delete some metadata for the IIS 7 located in the file applicationHost.config under C:\Windows\System32\inetsrv\config
From what I read on the internet this seems to be a problem in IIS 7 that doesn't delete metadata information about sites that are removed from IIS 7. Make sure to make a copy of the file before editing it.
Also start with my second recomendation before you reinstal frameworks wich is a lot harder for the system.
hope this helps