I fixed it, there seems to be a bug with the radeon cards. But I imported it with 800x600 and it worked fine. But when I save a city in 1600x1200 a small part of the city is gone.
I downloaded your Kupreanof map and its the samething. I studied your regions and all the large cities seems to have lost the last 1/10 of the city. There should be land or water there but there is nothing. But when i start one of thoes cities its all normal but the regionlook is wrong.