Well now, I used MapJack to raise the height, trouble is now the grass won't grow back and water won't flow in from the sea. Anyone want to let me know how to remove height? Or just edit the map so it works but still has a higher height?
Also, don't use the latest MapJack, it has a known bug when doubling map height (adds 256 instead of doubling). That's probably what it did, and therefore the map dimensions were no longer a power of 2.