Hey, I added Boot animation support for the topscreen to BootCTR9 with my last dev release, and to be able to ignore licensens changes I now rewrote it by myself.
My implementation in BootCTR9 uses the hardware timer to get the timing rigth and uses the arm11 to write it to the framebuffer, could some test if the timing is good? To use bootanimations set the splash to 4 and set the animation including its name as splash_image, and for frame configuration put a file with the same name as the animation + .cfw in the same folder. (example: animation.rgb -> animation.rgb.cfg).
If the timing is good I will clean my code up and push it to my repository, this way the timer could maybe be used in BootAnim9 too.