Luma3DS menu fails in some games

[naga_serpentis]

So recently, I've downloaded some updates for some software in Universal Updater, and I noticed that Luma3DS doesn't work correctly in some games like Monster Hunter Stories.
Whenever I launch the menu, the menu shows up for a frame and then goes away, but the game is still "frozen" and acts like the Rosalina menu is still open (it's invisible).

I'm using Luma3DS 10.2.1, I'm using a variant of it (which is included as a ZIP in this pose) which has more features which I like to use. This hasn't been a problem at all, but after updating the Menu is completely broken. Any way to fix this?

EDIT: This happens in all 3DS games.

EDIT 2: FIXED