First of all do not use maps in moddir (if my previous post wasn't clear on that, I hope this one is

) It does not work since terra incognita is taken from the map in standard folder instead of the one in moddir folder. Which is as yet unfortunately unfixed, to my knowledge even in 1.09.
Second, I do believe your map still has a small wrong 0-id ion the 2nd province from above (a small 'cloud' of TI indicates usually 1 or 2 wrong pixels in the game)
Third, you must always change terrain in province.csv to a 0-6 value before you import the map to the game. If terrain is 7-9 the game will recognize it as something else, like PTI thus. Also, if you specify a lake as terrain 6 (=river), it will get clouds of PTI on about 10 pixels from the coast to the middle (it is apparently a 'works as designed'-thing). Only if you specify it as terrain 5 (=sea) the TI will be gone, but then the lake will not be passable by armies.
Fourth, are you also sure that the provinces under terra incognita are udner PTI and not just scenario-TI? Test that with the 'columbus'-cheat. If they are under PTI, the problem is either terrain, or id-map.