#2 Jan 13, 2008 06:45
Have you tried via FTP or maybe cpanel to see if the directories are really there? I'm guessing that when you first visit file manager it shows you what exists for each blog (or user if you do it that way), then when you actually go to upload it shows you all the paths that actually do exist.
Does sort of sound buggish though. Like when deleting a blog it should deal with media folders for that blog, and potentially any content in those folders.