Yep. As I've read a bit more about this now, I definately have a merged rom-set. It's updated for 0.149 and it's been working perfectly everywhere, including previous versions of mGalaxy as far as I can remember, so I've been a bit fooled by that.
I wasn't aware of this until now!
I'll just take the "easy fix" and make some empty zip-files for the clones I use regularly. Or I could pull the clone roms out from the parent rom and zip them into a new file. That also works. Actually, it doesn't seem to matter what's inside the clone-rom-zipfile, as long as the file is there, and all the roms needed are found in the clone and/or the parent combined.
The best would probably be to get a complete new rom-set that's not merged... I'll look into that.
Anyways, problem solved, and mGalaxy still rules!
(But this merged rom-set works flawlessly with other frontends I've tested, so there must be a subtle difference in how clones are launched?)