Ok I know this is old but since I resolved the issue I wanted to post it here for anyone who might still be having it. You must turn on the option in the graphics plugin called Pixel Depth for this to get fixed. Kind of a win/lose though as doing this adds some wierd texture artifact around the water edge, so instead of flickering shorelines you now get some strange pattern. Oh well I'll take the pattern over a flickering annoyance. Maybe that other problem can be solved someday and its totally clean textures again
