I’m chiming in with my experience just in case more reproducers are of any help. I’ve encountered the issue @RavanH described in the initial post on my multisite install: files uploaded onto the root blog get url’s with blogs.dir while subsites (in subdirectories) get url’s without it.

I was running WPMU just prior to it getting integrated into WP proper, but unfortunately I can’t say for sure whether I did a clean reinstall or an upgrade to WP (non-MU) at that point.

I’m only running a single network with none of the plugins mentioned in this thread thus far. Well, no, actually I do run another multisite for testing purposes, completely separate from the first, and there this issue doesn’t manifest.

The upload-related variables for the main site are as follows:

`Upload Url Path:
Upload Path: wp-content/blogs.dir/1/files
Fileupload Url: http://mummila.net/files`

I suspect the Upload Path is what’s causing this; further evidence is that on the testing site Upload Path: wp-content/uploads results in url’s withoutblogs.dir.

I’m thinking of changing Upload Path, but I’m unsure where it ultimately shouldpoint to. If wp-content/uploads results in corresponding url’s, is that the default for the root blog? If so, is there a reason why it deviates from what the sub-sites have, which is sitepath/files? I’d expect the root site to have /files/ as attachment url base.