Right now on my N3DS XL I tested booting 9.0 sys with R, booting a GBA, quitting, opening again. Works fine (so the emuNAND firm is loaded correctly on reboots). This is with 5.1.2. Since you have a very complicated setup I'd advise to check you have the correct ARN path in the binaryAny emuNAND users with 9.2 sysNAND using AuReiNand?
How do you play GBA with AuReiNand? What options are set in your config?
Rather than me bugging @Aurora Wright I will attempt to get AuReiNand use info from people with a setup similar to mine.
If you have some time and have a setup like mine the help would be appreciated.
Edit: Please PM me so we can keep unnecessary traffic out of this thread. Thank you.