hi there.
this is strictly speaking not a wpmu problem but rather a general wordpress problem. still I hope I don't get bashed but rather helped :-)
I had a wp 2.6.3 blog in a subfolder and decided to move it to the root. moved the files, then used phpmyadmin to change all occurances of mydomain.com/wordpress into mydomain.com and also the relative path aka web6/web/wordpress into web6/web then checked .htaccess put the blog back online and now comes the problem:
as soon as I hit ANY page in the browser, CPU load goes to 80% even if it is only the back end. Put the blog into maintenance mode, deactivated all plugins except the maintenance plugin and still the same issues. Looks like there is some redirect taking place? Found this article talking about exactly the same issues while moving a blog from root to subfolder but the solution described does not help me: http://alexking.org/blog/2008/07/31/404s-and-wordpress-server-load
I see some other problems: all pages/categories work, except for the posts within the category pictures because it seems I also have a page with the slug pictures.
I remember there is a problem when there is a category and page with the same permalink and permalinks are set to /%category%/%postname%/ Any links for me to read up? Even changing the permalink structure doesn't help :-(