I experience the same issue
So far, I've tried:
* batch change metadata, so filename is same as version name
* made JPG master (vice versa)
* rebuild database
some files actually DO will relocate. When I manually add missing photo's (from the aperture-import-backup) to the master-directory, they will still not consolidate into Aperture DB.
You also see some "strage"-filenames passing by (Sf4dfAASDFGJ^W.JPG). most of the time the extension is missing from the file which Aperture cannot find.
When you try to 'locate referenced files' there seems to be no error or missing files
i looks like the database also holds 'another' original file name, which cannot be seen on the 'info' tab.