Just noticed that the hover text over thumbnails in the Files section of item records is a bit iffy.
If you upload an item and file manually to Omeka, the hover text displays just the filename, e.g. photo.jpg.
However, if you upload via CSV Import, the hover text displays the full location of the file, including the filename, e.g. http://www.domain.com/files/whatever/wherever/photo.jpg. Have confirmed that all else is well - the file gets renamed and added to files/original, files/thumbnail etc. It is just the hover text that is problematic.