I trust you are not adjusting the height of the terrain? If the terrain isn't high enough in addition to the amount of water then the land will not peak over the water. Adjust the terrain height to fix this.
I have a thread in the Support and Bugs forum talking about a problem that could also be what you are facing, the fact that it doesn't remember what height I have the terrain at, "Surface Data". So if I save a planet as a user object that has a terrain height of say 11 KM, it goes back to its default of 21 if I place the saved object in a new sim, or even back into the same sim. The same goes for normal saves, as in loading the save of a sim the planet is already present in also resets it to a default height of 21.
So this screws up the land and water ratio on my planets as well where I had the height to what I wanted to land to look like, but it forgets it. And no one ever answered a way to maybe fix it so I hope it will be in an update soon, I am sure its not just problems on my end.