Luckily I saved the original filenames. There doesn't appear to be an FAQ or wiki page about this. Apparently FB Alpha does actually use those specific filenames to ID the ROMs.
Renamed the ROMs, deleted the entries then re-imported the files back. Added the titles in the metadata and scanned the library for external metadata. The manually added 'Neo Geo' category was then replaced with 'NeoGeo' (not sure why the default name is 'NeoGeo', either, Wikipedia uses the space as does the 'Neo Geo Pocket' default entry).
However even after all this FB Alpha still fails to launch when clicking 'Play', giving the same error message. Any ideas what is wrong? If the command-line path is automatically enclosed in quotes (according to the example in Launchbox) it surely wouldn't matter if the path has spaces.
Edit: checking the 'Full file name without extension' option worked. Launches with some error message but after bypassing the dialog does ultimately launch. Not a smooth experience though, and unsure what the error is about, as it opens fine from FB Alpha directly. Any pointers would be appreciated for those who use the emulator.
Edit 2: for anyone interested the fullscreen settings needed to be adjusted. This wasn't apparent initially as after the error it only displayed the windowed mode.