The diagnostics upload tool uses the tmp directory to test the upload, it doesn't actually test it for the other folders vBulletin uses. My second guess is that your web-server or PHP doesn't have the right (group) permissions set to touch files in the document root.
You can refer to:
http://serverfault.com/questions/644...u-14-04-1-ngin
https://www.digitalocean.com/communi...s?answer=24893