For clarification, what kind of "updates" are you making to the areas?
As for the versions not matching:
If your versiond in the AdminCP, Wiki Admin Panel home page, and the wiki footer are not all showing the same number, then not all of the files were uploaded when you tried to upgrade. This tends to occur when you use a program for FTP and choose an option to transfer "New and updated files only" or something like that (it might be hidden away in your preferences). You should never choose this when uploading VaultWiki because you will always upload a file later than we last edited it and your server times will typically be different than ours, and this will lead to you having files from many different versions without knowing it. The "New and updated" option is really only good for files you have written yourself.
Download Alpha 4 again and upload it to your site, making sure you overwrite everything. Then, try to run the upgrade script again.
Once you do this, please let me know if the issue persists.