Could you say how far the land mass had moved.
There are 2 maps in the SH3/4 series, One a World map for looking at from 'space' and is fairly low res, and the other is for 'close-in' work. When zooming you might have crossed the boundary where the game changes the map it uses. This is seamless, but you'll notice it at about 8x (I think) when zooming in, the blocky map suddenly gets a lot more finer detail, and visa versa.
I've always used this finer map for creeping along the coastline and have no problems yet. Other than this maybe it is a problem for the area you're in.