Ouch! Been there, a lot, but things are going better on this end.
Funny thing is, last night I used the Make Map function for the first time (it's and update terrain) and the next thing I knew, cmpwater.bmp was updating lol. Good thing I didn't get too excited, because it didn't happen again. I figure it might have been a combination of Make Map and importing the water files.
I did see how the waterc file is impacting the water color. Turns out that black is the lightest ocean color and white is the darkest. The opposite of what I expected but if I'd re-read the Readme documentation, I've have known that lol. Doh!