I'm having exactly the same problem with every new game I import since my initial collection importing. When I originally imported my ROM folder, everything ran sweet both in Launchbox, and Big Box. However, when I import anything new, it imports fine, loads all the artwork etc, but won't start the game, it just crashes. The only way I can make new games work, is to delete and re-import the entire collection, then it sees the new games.
Running version 6.12 on Windows 10.