I can confirm that this problem exists in the newer versions of mkgmap. Some coastlines are missing in the map.
After playing a little bit with the data, I think it is the MP code thats causing the coastline to disappear.
It seems that the error occurs, when a coastline is member of to many boundary-multipolygons. In my test the coastline was disappearing when beeing member of more than two boundary-MPs.
So as a workaround: I think for boundary-multipolygons the multi-MP handling is not neccecary at all, because boundaries (normally) are rendered as lines and not as areas.
I hacked a little OSM preprocessor in vb.net (don't speak java) which does the following: change type from multipolygon to boundarypolygon for all MPs with no inner-elements. This eliminates the MP processing for those boundary polygons. If someone want's to get it, -> mail me. Chris