Thanks again @sleve_mcdichael. This will make the identification of the culprit much easier, but there is a catch: I will be away for a few weeks, but will definitely fix this end of June.
I was just asking for the ES version, to test on the same version, not that I was thinking ES has an issue.
After some thinking, I guess my oversight that the gamelists may also reside inside ~/.emulationstation/gamelists/ could be the cause of some if not all issues.
Setting the gamelistFolder to the same as the inputFolder and copy the existing gamelists to the inputFolder (i.e. sibling to the games) could be a workaround. However, it is a guess, I did not verify it by myself.