I posted this as a comment on a Git issue, but it's probably better if I put this here. Apologies if this is common knowledge, but I'm having issues running certain games with the AK2i kernel through the 3DS app. They run perfectly fine when launched through TWLM on the cart itself, which is what's confusing about this. Namely, it seems gen 4 Pokemon, Final Fantasy titles, Golden Sun, Metroid, and NSMB are all unable to be launched when the kernel is being used. They either freeze on double white screens, or in the case of Golden Sun, lock up on the "Loading" splash from the kernel.
I've tried several things to fix this, including formatting both of my SD cards again (I found they weren't formatted to 32k clusters, so needed to be done anyway). I could have sworn things were working fine up until I launched the DSi Browser to play around with it, but I could be misremembering. Something I've noticed is that it seems like games are trying to fall back on nds-bootstrap regardless of what loader is set. For example, DSi Enhanced games use it unless I explicitly set them to use the kernel through their own individual properties, and I've found .sav files next to my ROMs, which seems to be a behavior with nds-bs itself. I've tried doing this for the games that fail to run, but it's the same result. I've also totally reinstalled TWLM twice, making sure to wipe out literally everything when doing so, but this got me nowhere.
Hoping this is only a case of incompatibility, and I'm just going crazy. I can't think of what I possibly did to cause this, provided I'm not misremembering.