I have the same issue although I did not upgrade to 3.0 ! My blog is still in 2.9 and I did nothing special. But suddenly today it occured to me that all images dated 27/3/2009 or older have this issue : they are displayed neither in my media library nor in post galleries.
Their URL contains the site directory path :
http://www.ready.to.get.free.fr/wp-content//mnt/104/sdb/a/6/www.ready.to.get/wp-content/img_4650.jpg
Although the URL should be simply like this :
http://www.ready.to.get.free.fr/wp-content/img_4650.jpg
An example of broken gallery :
http://www.ready.to.get.free.fr/index.php/2008/05/un-soleil-estival/
I checked the database, all is fine. So it is a WP function which is playing wrong.
I do not remember what happened on the day until which are media are corrupt. Maybe it is the day when I checked the option to organize my media in year/month folders ??
Anyway, this has nothing to do with WP 3.0 or multi-site.
So maybe I should try black magic... ;) Or just wait ? :P