I'm running WordPress 3 on IIS7 and have multisite enabled. Everything is pretty much working, the first Media upload.
Here's what happens. If I click the Media tab, I get a 404 error on wp-admin/upload.php. However, if I create a post and upload the media item that way, it works. Moreover, once I've uploaded ONE image through the post mechanism, the media tab start working the way I expect.
I tried pre-populating the blogs.dir folder with the folder structure I observed on the site that had started working, but that didn't do it. I've check permissions and so forth also.