Found a solution:
Added/Removed/Moved the following in my JS:
var isWaterVisible = false; //added
onRepeat:swapWater //removed
function swapWater(){} //removed
water.css("visibility","hidden"); //added to buildAnimation() {}
tl.to(water.... //all moved inside of buildAnimation() {}
onComplete: function() {
if (!isWaterVisible) {
water.css("visibility", "visible");
isWaterVisible = true;
}
} //added to last to. of water molecule right after {alpha:0
and it works perfect now..