Can you remove *any* of the vanilla folders? Try going into the vanilla folder and removing the files and folders individually. I bet it's your conf files that are messing you up becuase they were created by Vanilla and hence owned by apache (not you).
Well, you're going to have to contact your hosting provider to figure out what's wrong. Vanilla is just files. It doesn't do anything to change it's own permissions (that's pretty much impossible on most systems), so it's something to do with your server.
Yup, the same thing happened to me but just to the files in the conf folder, they took on ownership by apache somehow. My ISP fixed it after making me jump through hoops to prove who I was and that I had a right to "own" the files.
I've had this happen before with a file uploading app I was using.
The app was creating files, and changing permissions, which ended up not giving ownership to me. Any file it creates I can not delete or change in anyway because I am not the owner.
Something to do with screwy group permissions or something. The way I got around it was by using another app called "WebAdmin". It is a .php file that can delete, move, files, etc... Since the ownership of the file was WWW the only person that could delete it had to be either the system admin, or a user of WWW, which this file would be.
I searched for a link but couldn't find an active one, so I zipped the file. Give it a shot, hope it helps. Just make sure to remove the file when you are done using it. Leaving it on the server would be a bad thing.
You can delete directories with that file I linked to. It also lists everything in the directory and allows browsing. Just dug through the code and it uses the unlink command. It just has a nice interface to use it so you don't have to code up a custom php file every time.