Yeah. weird. Somehow my Chalices doesn't like the wave when I turn the Wavebox on . One of them melt away . I try to point the pump upward instead straight out . Hope it work, because some how I have Red slime and bubble build up without Wavebox.
Waveboxes tend to stir up detrius that previous means of flow couldn't do... potentially you could be getting detrius settling on the chalice causing it to recede - just watch for that.
Generally speaking a WB will not harm any coral assuming the coral isn't being blasted like a tree in a hurricane (this goes for any type of flow, WB or not), and on the flip-side assuming the coral is receiving appropriate amounts of flow.