Part of the issue could be if you allow the importer to download from both the Launchbox DB and Emumovies. Launchbox may not be able to tell the difference between the two images. You could probably run a checksum on the images to confirm they are in fact duplicates. Though the image looks the same a slight variance would in fact make it not.
Running checksum on my arcade 3D boxes here is an example of Alien. Same image, one ending in 01 and other 02, and you see the checksums are different. I am not saying this is the cause for all duplicates, just something to take into account.