Case closed (for Recalbox at least): it is a bug in the fba-libretro core.
On the libretro/fbalpha-github page there is an open issue "[0.2.97.38] [RPI2] non-merged sets?" describing this very issue.
https://github.com/libretro/fbalpha/issues/80

@acris
I'm using non-merged sets and they DO NOT work as intended. If you use SPLIT roms, you need BOTH the CLONE set maglordh.zip and the PARENT rom maglord.zip to play maglordh. If you use NON-MERGED sets you ONLY need the non-merged CLONE rom set maglordh.zip and it SHOULD WORK WITHOUT having the PARENT rom maglord.zip.
Just using capitals for clarification, I'm not yelling at anyone!

@voljega
May very vell be a core issue.
All games I'm interested in (mainly SNK/Capcom/Irem) run fine and without lag on Rpi3. For example R-Type was too slow on Rpi2 but on Rpi3 it works very well with fba.

Hi there,

first, let me start by saying that Recalbox is awesome!
Now to the problem I am having: I am a long time MAME user and I know about correct rom auditing, the different possibilites of storing roms (split, merged and non-merged) and parent/clone relationships.
I prefer to use non-merged roms and I only keep one version of a game. For example, I would only keep and play the latest japanese revision of a Capcom or Irem game and delete all other versions. I only keep rtypej and delete rtype and rtypeu. As long as you use non-merged roms sets, a clone version should work without having to have the parent rom set.
The MAME 2003 core in Recalbox works as expected, but the fba-libretro core does not!
Even if you use non-merged sets the parent rom has to be present or else the game will not run and just quit back to Emulation Station. For example rtypej will only run if rtype is present. Or maglordh will only run if maglord is also present. But there should only be the need to keep the parent rom when using split roms. The reason for using non-merged sets exactly is to eliminate the parent/clone rom set dependencies.
Now, mame is working correctly with non-merged rom sets, but as it's a very old mame version I would much prefer using the fba-libretro core for all Recalbox arcade game purposes. I also tested the windows version of fba and that one works with non-merged roms. There really seems to be some kind of bug in the rom handling of the libretro-version of fba.