I fixed it myself.
- I deleted everything from the MIDI Designer folder on my iPhone.
- I started up MD on my iPhone, asked it to create a new layout for me as a starter, then shut it down again.
- I copied everything from my iPad's MIDI Designer folder into my iPhone's MD folder, choosing to keep both files if there was a conflict. I deleted the conflicted second copy files.
All fine now.
I'm not convinced that the problem as such was this specific layout that was loading at start up. I think it was more generic.