I only ever see it in Trainz Plus when I create a new route and the baseboard is at the default height of 0m, but I cannot recall when it first appeared. I have TRS22PE but never use it for route development, only testing.
It is a minor annoyance but no matter what height it defaults at there will be some height where it will conflict with the ground to create the flicker but that is easily cured.
On the plus side I do like the ability to add multiple water effect layers each with a different colour (muddy, ocean blue, algae green, etc) and surface effects. With the old legacy water you had a choice of one colour and one surface.