*.desktop files: The icon-position of an item is somehow associated with the internal (user) name of the item and not the actual file name. e.g. if u edit some item as a file, and change Encoding to something wrong/unrecognisable/non-UTF-8, after saving the icon will move at some default place (and not stay where u put it)
Yeah, the icon location is saved according to its 'display_name' field, which is usually the file name, but clearly not in the case of .desktop files. However, moving to use the filename will break the 'special' file icons and probably volume icons as well, so they'll need to be special-cased, which I'm not too keen about. Probably not going to happen for 4.4.
Marking WONTFIX. After looking at it, basing the position on something other than the display name is very difficult, and doesn't really solve the problem (renaming a file, for instance, will still cause it to jump). The only thing I can think of that would make this work correctly would be to base it on the filesystem inode number, but thunar-vfs doesn't give me access to that, and that might not work right on NFS-mounted home directories. Also, I'd still have to special-case volume icons and the 3 'special' icons, so I'm not a big fan of the idea.