oh just had a thought, are the missing auctions re-lists thru ebay? If so, it will not show active - I have no earthly idea why. I am noticing that when i relist thru ebay, the images on file do not show being in an active listing.
Good way to test it, try creating a new ad and insert images. When the image folder comes up - check hide images in active listings and see if those particular pics are there. I am re-doing ads that have been re-listed and need to go to my store, I use the hidden key so I do not want to see pics of items that I already have up.