I have been scratching my head for the past 3 days on a very similar issue, if not the same. The first run at LB was version 5.5 and at the time, I had imported my NES, SNES, and N64 collection to test and had 0 issues. On a new build (fresh install --> 5.7), I imported the same NES set used for Hyperspin (uncompressed) @ 791 games, a good chunk would not port over (as in 157 of them). Decided to finally hit the board and see what was causing the issue and found this post. It was mentioned a bug in 5.6 caused some issues with Emumovies preventing importing so I figured for grins, leave it off.
One of the games that did not import properly was Super Mario Brothers 3. This is what I have noticed:
If I use Emumovies, and drag/drop Super Mario Brothers 3 over, it gives a 404 error, asks if I want to import it anyways (I say yes) and then says 0 games were imported
If I do NOT user Emumovies, and drag/drop Super Mario Brothers 3 over, it ports just fine.
Super Mario Bros 2 imported without an issue so from a naming perspective, the only difference is the number 2 and 3. I tested 2 this method on 2 other problematic games with success. At this point, I'll likely just delete and add the set again without Emumoives (which I am a paid member)
Again, I've only spend a few hours here and there playing with LB and thus I've only imported my PC games and Nintendo sets (NES - Wii). So far, the only set experiencing this issue is the NES set which I suppose is why I'm a bit confused.
I've attached an example trying to import Super Mario Bros. + Duck Hunt + World Class Track Meet game using Emumovies