Well...
I don't think I should have a nitrate problem either, but I have my theories...
#1, I used 100% base rock for the main display (180lbs). This baserock was from reefer rocks and is extremly porous and looks very nice. However, I believe it might be 'too' porous and not have a big enough oxygen free zone as traditional dense LR from the ocean. This would lead to a reduction in anerobic bacteria and an inherent inability to deal with as much nitrate conversion deep inside the LR.
#2, 1"-2" Sand bed. I did not want to go with a DSB and did not want to go with barebottom (at the time) Now I'm wishing I would have gone BB, as the detritus buildup would not sink into the shallow sand bed. The same problem as noted above essentially... Deep enough to convert to Nitrate, but not further.
Note: I have more tank inhabitants than I posted above, those are just the bigger ones... but you are right, it "should" have been fine. Tank has been setup and running for over a year and a half. Nitrate is anywhere from 50-100 depending on what's going on. (recent water change, etc)
Picture of rock for reference:
