The problems that I have noticed with the plugin, so far, when used with WPMU 2.6.2 is that:

• When you write a post and upload a picture via the Media uploader, the image uploads fine, but when you try to embed an image into the post: the Media uploader frame goes blank and the image is not embedded in FireFox and Safari; or you get a host of security error messages and permission denied in Internet Explorer and then you get the login screen.
• In the Write Post screen, when you try to “Add New Category” and click Add, the new category is not created.
• The Flash Uploader reverts to the browser uploader (uploading multiple files vs single files) for the first picture uploaded, but changes to the Flash uploader afterward.
• You will sometimes get a funky error when trying to activate/deactivate multiple plugins simultaneously.

I’m not 100% sure, but I think with WPMU version 2.6.1 and previous, the Domain Mapping plugin worked completely, but since upgrading to WPMU 2.6.2, it’s been a bit off.

From what I can tell, it has something to do with authentication. For example, http://buiphotography.com is mapped to http://buiphotography.bui4ever.com. Based on what Donncha designed the Domain Mapping plugin to do:

The domain mapping is for blogs only, not sites. The domain mapping hack always annoyed me because it mixed the two concepts up so much. Donncha

What that means is that http://buiphotography.bui4ever.com is the actual site. When you domain map http://buiphotography.com, both the URLS continue to work on the back-end (WordPress Dashboard/Administration Panel), but anyone visiting http://buiphotography.bui4ever.com, the URL will rewrite to http://buiphotography.com.

I think the problem lies in that you if you login via http://buiphotography.com/wp-admin/, the cookies do not populate to http://buiphotography.bui4ever.com. Some where there is where the media uploader is not getting the correct permissions. So I’m not sure if this problem existed before WPMU 2.6.2 or after.

There is one solution, but I personally (and I imagine Donncha) don’t find this the best solution, but it works. Andrea R. suggested editing all the blog fields from http://subdomain.domain.tld/ to http://domain.tld/.

UPDATE: All the sites are now upgraded and running WordPress Multi-User 2.6.2.