I wrote an article on my personal blog about fixing 404′s on WordPress Permalinks on an IIS 6.0 on a Windows webserver. There were two different sources I got the 404 from and which I had to fix; first from WordPress and then (Murphy’s law working here ;)) also from IIS. I hope it can help you if you have the same or a similar WordPress problem.
Now at TTY we prefer setting up systems with open source software and therefor using servers with a Linux flavour and an open source HTTP server, but there may be situations where a Windows and IIS system is already in use. This article shows we are capable of handling just that.