OK, then it sounds like you have something configured wrong, after seeing this thread i just imported my FBA romset and its working just fine. I dragged my FBA romset onto Launchbox, i called the platform FBA and told it to scrape as Arcade. I chose Retroarch as the emulator, and on the last page of the wizard told it to import as MAME for non MAME emulators and imported. In Tools/Manage Emulators/Retroarch/Associated Platforms i have a FBA platform with fbaneo_libretro selected as the core.
Games load just fine.