I am having a similar issue in completely different circumstances.
Aperture sometimes imports fully, but often imports every 2nd photo, then skips two, gets them all for a while... randomly!
I tether my Nikon D4 via ethernet to a Mac Pro (1,1) using the Nikon software
into a folder, to which I attach a "Folder Action" through the mac OS (10.6.
telling Aperture to import the contents of that folder to a project "AA Rename" in Aperture
The images are all there in the folder, Aperture just doesn't import all of them.
"Do not import duplicates" is unchecked.