I have the following script:

Tweaker.setPlacementStage("POST_POPULATE")

muddyBiomes = forAllBiomes()
muddyBiomes.registerGenBlockRep("biomesoplenty:mud", "minestrapp:mud")

And there are no other replacers for this block. The result has certain areas in which the replacer isn't applied.

In this screenshot the darker mud is what's supposed to be there, and the lighter grey mud is what is meant to be replaced:

The edges of these patches seem to sometimes line up with chunk boundaries, but then other parts of the same chunk will have the replacer applied correctly: