If you want avoid the effect, you could use just two waves 4 pixels tall, going back and forth. Probably the best would be add a black line under the 3 lines now used for the first two waves.
If you can spend more time and tiles on the issue, the rule more or less would be that the crests of the waves plot a sine wave animated across the sea tiles.
I'm not sure what you are suggesting. I have tried different versions and none of them really works well.