Can you do the following:
Delete the Atari 2600 platform (right click it on the left and press delete, say yes to both windows
Run the Atari 2600 rom import again, on the page that lets you pick various options like force import, combine games, etc make sure there are no checkboxes checked. Also do not download media at all.
Ensure the number on the import wizard's last page still has the correct number of files reported.
Import the games and see what number you have.
If less than the number of files then zip up your \\LaunchBox\Data folder and send it my way via PM