The people having issues with GBA VC injects and DSiWare games, what are your 3DS models and what are your Luma configurations? I'm using a 2DS to test all of this so maybe you're all on N3DSes with Clock+L2 enabled in Luma? That's the only thing I can think of.
Here's proof just so no one thinks I'm lying.
i have a N3DS XL but without L2+Clock enabled to