Josh:
I'm running Win2000 and IIS5 and have the same issue. I went ahead and started using the php.exe file under the CGI settings, and was able to get that to work. Unfortunately, CGI on IIS has a performance decrease, and I have some trouble with garbage characters popping up on my output html once and a while. I'm hoping that the ISAPI setup might fix these issues if I ever get it running. Maybe someone else out there knows how we can fix this?
Jack