I deeply appreciate the help and your taking the time to to reproduce my issue. It seems as if there might be something internal in Aperture Relocating Masters that is sometimes not recognizing changes in the Version field when it is changed after importing.
I just did another import. The first troublesome file's Version Name field after import is 20110113_04003.JPG.
I completely deleted 20110113_04003.JPG in the Version Name field and then typed in Test. I only selected the single image rather than the entire import group and chose to Relocate Master using Version Name for the Name Format. Aperture used 20110113_04003.JPG for the file name rather than Test.
I tried exporting the same file to see if that might shed any light on the matter. I exported the master choosing Current Version Name for Name Format in the export window. The file was named what I had entered subsequent to import in the Version Name field.
I then exported the same master file choosing Master File Name for the Name Format. Aperture used the file name assigned on import, 20110113_04003.JPG, rather than MasterExportMasterName which was currently entered into the Version Name field in Aperture.
Next I tried exporting a version of the file using Current Version Name for Name Format in the export window. Aperture named the exported file using the changes I had entered into the Version field.
I ended by choosing Version Name rather than Current Version name for Name Format when exporting the same version of the file. Aperture also used the the changes I had entered into the Version field to name the file.
Aperture is correctly distinguishing the difference when exporting masters but gets confused as to whether to use the original import name or the current version name when relocating masters.
Renaming the Version Name when viewing the master as opposed to viewing the version didn't have any effect on what Aperture chose to use for a relocated master or exported filename.
File Name Example in the Relocate Masters window always indicates that it is using the original import Version Name rather than the changed Version Name even when it names the file using the changed Version Name.
I've learned some interesting stuff about Aperture file naming but remain baffled as to why it chooses the original import Version Name to name some files when Relocating Masters and chooses edited Version Names for other files.