Seems like it doesn't work with just one animation file for the top screen.
I'll try to be as helpful as possible with my setup:
I'm using an old 3DS, 10.7 sysNAND, 3.13 AuReiNand, v0.3.2 BootAnim9.
A9LH payload file is named arm9payload.bin on root of SD. BootAnim9 is named arm9loaderhax.bin...