Here are some of the answers that might prove useful. This question describes a problem where you want to have land bridges connecting player islands that boats cannot sail through. Obviously, using Shallows won't prohibit boats. Usually, in this case you forgot to transform the beach terrain into your land bridge terrain.
Beach is pathable by boats.
There is probably a typo in your Random Map Scripting file. It may help to isolate parts of the script to identify where the problem is. The Random Map scripter was not a feature we developed and extensively tested. It is a freebie that we thought you guys might appreciate poking around in. I would test it both ways and see what works.