Is your topographic data accurate, and does it extent into deep enough water to capture all of the refraction effects?
You mentioned the slope is really mild...if by this you mean there is a flat offshore profile, then you know that large long period waves will be affected by the bottom far offshore, potentially miles offshore if depths are shallow enough.
You mentioned that you aren't seeing any bottom topo irregularities in the vicinity of the breakwater but how about further offshore? For large, long period swell a bottom irregularity in 20, 30, or even 50 feet of water could have a large effect on wave height, although at these depths you wouldn't expect the tidal swings to change things much, but in 10-20 feet of water it could be significant. What is the tidal range in this location?
I'm way out of my wheelhouse here but do the questionable results involve average or peak wave heights? Does the model take into account the waves reflecting off the breakwater then running into the incoming swell resulting in doubled up waves?
Depending on the tide, the resulting wave peaks could be much higher when the tide is at a sweetspot that allows the swell to reflect off the wall with max efficiency which in turn would cause bigger backwash type peaks. But, they would quickly subside and not affect the breakwater very much.
Again, way out of my wheelhouse but this question had me scratching my head.
The City of Boynton Beach, FL wanted to extend the north jetty at the Boynton Inlet (South lake Worth Inlet). It is one of the most dangerous inlets on the East Coast with the exception of the Oregon Inlet in the Outer Banks. It is very narrow, and on an outgoing tide if there is an east wind swell and an onshore wind, the volume of the outgoing water will stand the incoming waves way way up. The inlet curves at the mouth, so you can't see what you are getting into until you are in it, and if you try to turn back you will be broadsided and capsize. It has happened often, with loss of life on rare occasion. Inexperienced swimmers constantly get sucked out and some drown there.
There was an outcry to lengthen the north jetty to make the inlet safer, at considerable cost and environmental impact. It was determined after lots of data modeling and back and forth between fishermen, lifeguards and city officials, that it was a fifty fifty chance that the project would do more harm than good. Refraction off the longer jetty was a big factor in the decision to scrap the project. Cooler heads prevailed.