unanswered Pokemon Fire Red Fly Black Screen on the 3DS

[greenDarkness]

So to begin I started with a Pokemon Fire Red Rom v1.0 and I patched it with these patches.
Throwback: https://www.pokecommunity.com/showthread.php?t=285094
FireRed AGB_FIRM Save: https://filetrip.net/3ds-downloads/...ix-pack-for-pokemon-gba-games-1-0-f33538.html
Physical Special Split: http://www.mediafire.com/file/b4j6b4p1rq94l67/PhysSpecSplitFR1.6.ips
Move Affinity: https://dl.dropboxusercontent.com/u/79534548/Hacks/Pokemon FireRed - Split Move Affinity Changes.ips

I progressed in the game with no problems until I got HM02 Fly. Whenever I select a town, the screen black out, and I'm unable to do anything. 

I extracted my save with decrypt9, and then restored the battery to the rom that I built the cia from. Upon restoring, I was able to fly normally. 

Does anyone know what is happening, or what I can do to fix this?
Thank you!