Even though you removed 3.319 it does not change you settings. When you installed 3.321 you should have seen a screen telling you to go to a link on MTU's web site and follow the instructions before proceding with the install.
What you have set-up (file and folder locations) is not correct. You need to change some of this to prevent Vista from hiding your files, including the database files, your playlist files, etc.
You need to follow the instructions on the following link to protect your files from Vista:
http://www.mtu.com/upgrades/hoster/vista-upgrade.htm
While your at it, I would move those upgrade files to the new location too so you won't lose them.