Just in case anyone ever finds this in a search....
Flags werent the problem, it was the fact that the "coast" and the next set of altitudes over were extremely opposite(lots of little contour lines!), so by making a more even transition, the black stuff went away.
But I did find out another case in which wrpedit displays that black texture thingy... If I set a group of selected altitudes to "flat" and raise those altitudes above sea leavel (They were previously under the water level) the ground is covered with that black. If I add hills to the area, the black goes away.
I think this might be something to do with the video card on this laptop I'm using, but just incase anyone searches and finds this, i wanted them to find out my results.