That's probably a blessing in disguise. I have read 'way too many posts from folks who "thought" their photos had been properly imported, and the camera automatically erased, and then found that the photos were, in fact not there. I always leave the photos on the card until I am sure that they have correctly imported, and then I manually erase the card.
Don't know how to fix your problem, but if I were you, I would not consider it a problem. Just go with it.