Unity 2019.4.9f1/2020.1.6f1, MM 2.0.8
When using more than one texture mask for VSPro, MM applies the texture mask numbers in the wrong order causing the textures to be shuffled.
I found the problem being around line 83 in VSProMapsOut.cs, where you use i / 4 as the index for the maskGroupNums assignment.
Changing the line to this:
maskGroupNums[output.maskGroup] = output.maskGroup;
fixes the issue since you use the same indexing for the Color[][] array.