Now I'm curious. Is the pattern aligned to vertex coordinates? Screen coordinates? For such patterns I'd pin them to screen UVs. Has the downside of the pattern not moving, but it also won't flicker (and it's kind of what I expect from Flipnote animations).
The dither pattern is 100% in screen space, but if you don’t offset the pattern, the verts “slide around underneath” the pattern creating a lot of flicker and aliasing, so I work out how much the center of the camera view has moved in screen space each frame and offset the dither pattern by that.