I've heard that rumor too....I don't have a Wavebox (yet) but I've seen a couple in action and I'm kinda skeptical that it would damage a properly built tank. Has anyone actually seen this happen?
If you're worried about it, I would recommend using a Tunze 6100 Stream instead (or 2) in conjunction with the Single or Multicontroller. The controllers can ramp the pump output up and down and produce a wave effect, although it doesn't cause all the tank water to pull back and forth like the Wavebox...I have used these, and they're awesome. They give you a lot of water flow without any whipping currents