Came here to post this.
Happens to me too, on latest Atmos and FW, thought maybe it was a problem with a recent update but guess your setup proves otherwise.
It seems it could possible be a problem with CFW? I saw at least two playthroughs on Youtube where the problem doesn't happen, granted I don't know what these people are running, but since they were uploaded on release day, I'm gonna assume it's stock firmware.
Here's an example you can see very early in the game, on the shop, at 24:38 :
Compare that to how is running right now for us and you should see a significant difference.
Problem happens in both dock and handheld mode too, not sure if overclocking would ease it somehow, haven't tried myself.
Sorry for being offtopic, not sure if this enough of an issue to warrant a separate thread.