Aside from the Featured Images Lightbox issue, I've come across a problem with Galleries, and with the text editor with Newscast running Wordpress 3.1 on a Multisite installation.
When I embed an image gallery in a post, only the Featured image displays a full-screen image correctly. Clicking on any other image in a gallery results in the error:
Image cannot be loaded. Make sure the path is correct and image exist.
I believe this is because of how multisite stores images (in /bin/[blogid]). I haven't had a chance to look at the code in detail, but I wanted to make sure it was reported, and hopefully fixed more quickly than I can (my time is extremely limited).