I’ve done a bit more experimenting now, still the problem persists.
It seems that the "Resource path" and "Resource URL" don’t do anything, it doesn’t matter what the content is, the links to the displayed files still stay in the same format:
http://sitename.net/www09/manager/..%2Fassets%2Ffiles%2Fextra%2Ffilename.doc
As you can see the "/manager/.." part should’nt be there.
Only changing the "File Manager path" seems to work as intended.
Any ideas why? I’ve tried changing both the user configuration and the system configuration, but no luck.
Could this have something to do with friendly URLs?
One more strange thing: I can delete the files just fine from File Manager, just the "Download file" button (floppy disk image) link is wrong.
EDIT: I’ve also tried putting files to another directory and changing the permissions.