scrolling warp - palette problem

I have some water tiles colored with both cset 0 and cset 5, they are the exact same color in the palettes, and in the same position.
When you go through a scrolling warp it changes the water tiles placed in cset o to a lighter shade.
How it's doing this I cant seem to figure out, like I said they are the exact same colors in these two csets.
It's worse when you scroll from one dmap to another using a different palette, even though the water colors aren't even in level palettes.
It's done it with a normal scrolling warp, and a scrolling warp set to insta warp with open effect.