Thanks for the advice!
Interesting to learn about the 'Visible software-lists' options. I wasn't even aware they existed. As it happens, that wasn't connected to my problem.
Clearing the software-list cache fixed most of the problems. 'Checking software-states' now shows all the software list entries that should be there
Most of the software list Favorites are there, but strangely, not all for every system.
To investigate further (and learn more!) I found the database you referred to, called mame-user-data.db here on Windows. Unfortunately neither MS Access 2007, nor LibreOffice Base wanted to open it. Opening it in the Wordpad text editor however does show what appears to be names of all the Favorites, including for those systems that don't show up in QMC2. I suppose that means that they're there, but not being displayed for some reason.
As for remembering what changed over the past month or so, that's tricky. I'm a casual user and don't delve into every system on a regular basis. That means I don't know when the problems emerged. If you remember back to the previous version cycle, I ended up using the Win7 x64 builds of QMC2 that you kindly made for me. Annoyingly, I don't know if what happened, happened before that, after I using those builds, or only after the most recent stable releases of MAME & QMC2.