I haven't looked at what the plugin actually changes yet.
Perhaps there's a documented "fix" somewhere that I missed? I see two different answers and tomerk still hasn't said anything about it. I think I'll wait.
http://i56.tinypic.com/2dnjtd.jpg I took after the initial release, showing the "blue paint syndrome." When I asked if there was a fix, tomerk suggested the floatSinBoverSinA change detailed above. Doing that eliminated the issue to a degree, but it comes with the trade-off of messing up transitions between above and below water, I believe (tomerk can explain it more thoroughly)
After the next update, tomerk suggested changing the value of inScattCoeff to 0.15 from the default of 0.20 (not 0.5 as mentioned above, that's incorrect) instead of changing floatSinBoverSinA. This similarly minimized the "blue paint syndrome" by making the water darker. Because it doesn't come with the issue that the earlier "fix" comes with, and makes the water darker and purely reflective similar to Enhanced Water, I've stuck with it and really enjoy it. So http://i51.tinypic.com/23k95bp.jpg from my current game, where I'm using a inScattCoeff value of 0.12 (as well as increased transparency and slightly reduced ripples). (also note to tomerk -- one of the six million screenshots I'll send you soon enough that you can choose from to advertise the mod on tesnexus)
Hopefully that answers your questions about "blue paint syndrome" and what can be done about it. Of course lots of people prefer the water that way, so I don't like characterizing it as an issue with the water, it's all really personal preference.