I was using Luma 5.5 before, after update it to Luma 6.1.2.
My theme choice couldn't show up, every time N3DS reboot will change back to "no theme".
Booting up with Luma 6.1.2, getting a "no theme".
Change arm9loaderhax.bin back to Luma 5.5, boot up again will get the correct theme I set...