I also had a problem with drag and drop of the widgets after enabling wordpress 3.0.1 mu.
After disabling all plugins I found out that the hRecipe
(https://tinobox.com/wordpress/hrecipe) broke the drag and drop.
The drag and drop did work on the sub-pages (xx.kookblog.nl), it was only the main page (kookblog.nl) where drag and drop was broken.