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Just for the record, I can see exactly what's happening... Zygor was also displaying the unexplored areas on your map, but does not color them. If you look at the map while Zygor was active, you'll see the areas that MFWM identified as unexplored are displayed while Zygor was active.
Now... the funny thing is that mods are loaded in alphabetical order and, apparently, execute in that same order. (I haven't proven they execute in the same order, but it does appear that way) So, MFWM was displaying the unexplored areas and tinting them, then Zygor overwrote what MFWM did.
You had two mods trying to do that same thing at the same time, so whichever one did it last was the only one you saw. I'm guessing the option you found in Zygor was one for whether or not to show unexplored areas.
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