The VM2 does create a file with the game title - but this applies for the automatic detection with GDEmu + OpenMenu. The general automatic detection (GameID) works differently, so this cannot be applied.
If a game is not in the list, then the GameID doesn't work (unless I add support for a game via a firmware update).
Only OpenMenu gives absolute flexibility to this and 100% coverage.
Now, the fact that the GUI fails for you, is what bothers me most. There have been a couple similar cases (only 2~3) having the same issue. I have tested the GUI on 5 different PCs and everything's working fine to me. There might be a detail, relative to your PC (OS, drivers, etc.) that's causing it.
So, since the GUI gives you all the tools to easily manage your uSD, I would suggest on focusing to solve this issue instead.
Please, let's transfer this in private, so we can discuss things until a fix is found.
P.M. me at :
[email protected]