I'm having this problem too and the duplicates tick doesn't help.
In my case, I'm only missing like 1-4% of any system, but it doesn't make sense because I don't have any clones or multi-regions (1G1R). I'm validating all roms with the latest No-Intros.
I can't even tell which ones are missing because for example, it'll see 588 of 595 roms. Retroarch sees them all and so do RomCenter and others. Launchbox is the only one with this issue.