I was having a problem with this on a map I'm making....
I read a day or two ago that make sure the terrain scale is a power of two (2, 4, 8, 16, 32.....) and make sure the positioning (the location in numbers) for the water block is a multiple of 8 (8, 16, 24, 32...just take a calculator and divide by 8 and change it until when it is divided by 8 it is a whole number...)
That is untested but will hopefully work...