***quick update enabling a framerate toggle via msi/rivatuner to cap it at 30 fps also makes the cog function and if you toggle back and forth it would start and stop spinning, so this is a simpler solution meanwhile and it's similar to how in earlier versions we would have to do this method for when cutscenes hadn't been fixed yet***
So as others have stated and as I just came to witness it myself seems as though the 60 fps mods in general break physics or so. To test what I'm experiencing go to Turakamik Shrine located b4 exiting the valley into the Gerudo desert. There's a large cog that's suppose to be spinning right before the last section of the shrine but it doesn't with the 60 fps mods enabled you can ultrahand it and wiggle it to break free and reattach and it stutters as if trying to spin. Anyway I went ahead and ran the 30fps static mod to see if that would fix it and it did its spinning along with the rest attached to it when at 30fps. In this case it's not a big deal as use of the cog is to get access to a chest above but it has potential to ruin or make other similar ish puzzles within shrines impossible if a user isn't aware the 60fps mods are the culprit for which they can't progress any further anyway if you could look into said issue that would be great for those trying to stay at 60fps.
(Ryujinx, docked mode, vsync enabled, resolution scale 3x, vulkan, graphics backend multithreading auto, post processing affect none, upscale bilinear, anisotropic filtering 16x, 16:9)
(Rig specs 3090ti Fe, 13900k, ddr5 2x16 32gb 6600)
Mods being (normally) used
-60fps blackscreen fix from elsewhere
-dynamicfps++
-visualfixes1008p_fxaa_on_fsr_off
-visualfixes_anisotropic fix
-visualfixes_disablequalityreduction
-visualfixes_shadowresolution
-graphics-island fix from elsewhere