I updated to atmosphere 0.9.4 with sys-clk enabled and the CPU-GPU clocks are stuck in handheld mode speeds, all the games stuter pretty badly, every time I boot a game the clocks goes down and the only way to recover dock speeds is undocking-docking the Switch.
Disabling sys-clk every game work fine.
I double checked my config file and it happens even with games that are not in the list, a workaround is explicity the dock speeds in the config, but it's annoying having to configure out alot of games.
EDIT: I fixed it, it was a problem with qlaunch sticking its clock speeds into the game, that's why it always happened at first boot and not in middle of gameplay.
If you are using SunTheCourier's sys-clk-Editor make sure to set qlaunch title in dock mode speed, as reseting it will set it in handheld mode speed and carry that speed to the game.
Just get rid of your config file, it's probably corrupted now which is the source of your problem