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 on root of SD. I have a folder called 'Anim' on the root of my SD. I put the animation files onto there.
I've tried two different animation files but only one is working. The working animation is the N64 from here:
https://gbatemp.net/threads/a9lh-bootanim9-animations-thread.420421/ The non-working animation is from /r/3dshacks here:
https://www.reddit.com/r/3dshacks/comments/4bvj14/ (scroll down a little, it's called normal one download)
The N64 animation worked immediately with only the two files provided. No config file added.
The A9LH animation from Reddit has only one file which I placed as SD:\Anim\*here*
It didn't work but after I saw there was a config file (20fps) linked below so I got that and placed it as SD:\Anim\Config\*here*
Again that didn't work. It played the animation and hung there and didn't boot into my sysnand.
Maybe I'm doing something wrong but I'm not sure. I've read over your post many times now. :s