I had the very same problem, but I also have a fix. Delete the uploads folder entirely via ftp. Then create it manually and make it writable, then inside the upload folder create the year folder for 2005 (and 2006) and make writeable, then create the month folders inside of these years (1-12) and make writeable. WP should allow uploads now. Bit of a hassle but it works until we can figure out the real problem.
