Was the bug that water nations don't work present in the Dom II version, or is this Doms3 specific? If so, how hard would it be to fix it? I have Gimp; dunno if that's any good for this.
It's a bug in Dom3 and the option to let the game assign random nations. The random selection does not take into account that some maps do not have water provinces to support water nations. It ignores the map setting "#seaplayers 0".