Maybe try disabling all the mods, and enabling them one by one (with scaler enabler first reactivated), to make sure it's not a problem with one of the other mods.
I also attached a copy of the 5 mods I use, in case one of the ones you have is the problem (they're also gonna have the assorted versions of the mod for older builds of the game, since I didn't sort out just the v2.1.0 ones).
Here's my settings, and I have no problems like you have (Oh, and I'm currently on Yuzu EA build 3352):
View attachment 387509
View attachment 387510View attachment 387511
Oh, and my Audio driver is set to 'sdl2', because I got some audio desync in xenoblade 3 with it on 'auto' or 'cubeb'.