Okay. I assume the problem is with the TwlBg patch (either Sono's or the one that my patch applies at runtime).I tried the 2.4 version and when I gain control of Yoshi at the beginning the game starts auto pressing everything and only stops if I open the pause menu. I'm using a New3DSXL btw.
Do you have the last version of TWPatcher installed? Have you tried some other patches like widescreen mods and screen filters? This problem may happen when there is no patched "TwlBg.cxi" at "/luma/sysmodules" at all or the option "Enable loading external FIRMs and modules" is off in Luma's settings. Could you also try some of my previous versions (those 3 others in my first post at the top)? And if none of it works, I'd like to know your game and OS versions (for statistics)