So, I have no idea why, but if you use the color #99BFFFC0 for the water, it will be fully opaque.
Meanwhile if you lower the red value just a little, like #79BFFFC0, it will have the transparency set correctly based on the alpha value.
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Sorry it took me a while to get back to this. It should be fixed in the next release. We were using 32-bit integers when parsing that color code, and that caused an overflow.
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