Have you tried running the installer as Admin?
Yes, I'm logged on as an Administrator and I have used the option "Run as Administrator" on both the installers, and the Web Server Configuration Tool. Same outcome.
I'll add this...
When I first start the wsconfig tool, it creates the wsconfig tool inside of C:\JRun4\lib\ and extracts the jrunwin32.dll file into that directory.
But that's where it hangs.
Ah, running MultiServer? Must admit I've never done that. Certainly CF9.0.1 will run on Server 2008 R2 SP1, because that's what I'm running. From my build notes, there doesn't look to be anything special. We do run CF as a named user, are you doing this? If so, does the user definitely have the right permissions?
Apologies if I'm preaching egg sucking, it's just sometimes the simple things that catch you out
If you can't get it working I'd try doing a standalone install rather than multiserver, see if that gets you anywhere.