Update: Fixed thanks to your advice smile
What happened and how did I do it?
Opening the existing mame-user-data.db in DB Browser for SQLite was interesting. While it had records for Favorites for most systems, the systems I was having problems with didn't show up at all.
I think the file must have been corrupted or truncated in some way. Possibly connected to some QMC2 crashes that happened last version when I would open the softlist. Incidentally, I didn't report those crashes here because it was intermittant and I wasn't able to predictably reproduce them. Those crashes have stopped now with the latest version, btw.
Back to fixing things. Fortunately I learnt from last time I had some corruption. A few months ago, I have a corrupted mame.fav after some power supply disruption. Since then, I learnt how to mount the image from the Windows 7 image backup. So I did that and retreived a previous copy of mame-user-data.db. Opening this one in DB Browser for SQLite showed that the corruption/data loss must have happened in the last few days because the missing records were there! All I had to do was export some recent additions from the somewhat corrupt copy into this un-corrupted backup file using DB Browser. Then put that file where QMC2 expects it to be and test. And it worked! Everything is appearing the way it should do and nothing is lost. All back to normal now smile

What have I learnt from this?
That clearing cache is the QMC2 equivalent of "turning it off and on again".
That it's a good idea to reguarly save backup copies. That's a process I'll get into the habit of doing!
And it was really interesting seeing how QMC2 stores it's data in SQLite!