I found another issue when doing this.
Since there is a .lha and a .uae file for each game, it shows 2 entries in RetroPie.
I solved this by renaming the .lha to .l (any extension that RetroPie doesn't recognize will do), and then editing the .uae file to match that extension.
If anyone knows a better way to do this, please let me know.
In general, I have no idea what it was, but ... I once again updated the retropie setup script, and once again uninstalled and installed amiberry from the sources. And (magic) everything finally worked as it should ... amazing (sarcasm)