If homebrew is launched directly after NSMB 2, GPU commands aren't being executed anymore

[KonPet]

To reproduce this bug just launch New Super Mario Bros 2, and afterwards any other homebrew game. Now, after initializing the GPU, no gpu commands (like GX_MemoryFill) seem to go through. The functions also never return any errors. And as soon as you start doing more stuff, like drawing a frame, the gpu crashes completely. Despite trying for quite a while I wasn't able to figure out how to fix the crash, I simply don't know enough about how the GPU works.

[DeltaF1]

I think I just reproduced this on my N3DSXL.

1. Launched NSMB2
2. Pressed Home
3. Launched mGBA from the home screen
4. Pressed (A) to confirm closing NSMB2 and launching mGBA
5. The homebrew animation plays, then a black screen, then the screen is covered in noise.

I was able to take a screenshot with Luma but could not exit the application with the home button and had to use the Luma menu to reboot.

[kynex7510]

The game seems to use undocumented GPU registers, maybe the issue is related. The attachment has them, though I don't know if there's more.
unk_commands.txt