I managed to solve this by updating manually to the newest version of WordPress.
I already tried this and still no cigar. The files are being uploaded to the server, but for some reason WordPress does not see them. The issue must be on WordPress’s end.
Even when trying to update WordPress, I get:
Could not create directory.: …./wp-content/upgrade/wordpress-3.tmp
I’ll update manually and see if that does it.
Same issue, same date:
The uploaded file could not be moved to …./wp-content/uploads/2013/01.
Most likely a file permissions issue because a new folder would have needed to be created for 2013. Ill let you know if I find anything.