I'm now using CTRPF with 804MHz clock on a New 3DS and the 60fps codes still won't activate. The code to give everyone tutti works fine, however. I'm using the CTRPF release linked in their GitHub which redirects to this release thread: https://gbatemp.net/threads/ctrpluginframework-blank-plugin-now-with-action-replay.487729/
To be honest, i dont know why is not working for you, but until know i was the only one that tested it, so maybe only works for my gameplay. What version of the game are you using? Whats the title id of the game? Are you using an undub version of the game?
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I just start a fresh new game data, and the code still works (only on gameplay, the code doesnt affect the videos). Also im using the .3gx version of the ctrpfplugin with luma plugin loader.