I feel a bit stupid to have to confess this but I think all my issues are explainable by user error. There is a (very small) chance that there are others as silly as myself out there so for their benefit I can summarize what I have found:

• Aperture seems to honor the "reject" flag during import even if it is set by another image management application. I have tried different tools over the years and apparently used the "reject" function in those.

• The reject flag seems to mean that Aperture ignores the file in all subsequent operations, export, relocate, consolidate etc. Which of course makes sense, really.

• The "don't import duplicates" works and if you have had less than stellar control of your workflow in the past you may have dupes in your image file hierarchy.

• When you let the finder count your image items, it includes the thm-files from video clips, Aperture doesn't, of course.

• And finally, the most embarrassing one - when you juggle different disks and versions of your image tree (you have backups of course) make sure you are actually importing from the same tree that you are looking at in the finder!

So with a red face I will now just trust Aperture to do the right thing and retire to be one with my shame...