Do you have a TDS meter? Nitrates are part of the total dissolved solids and therefore would show up in your TDS number. In addition, RO removes nitrates, with the DI grabbing any that are not removed by the RO. So if you're seeing nitrates in your water, the only way it could be coming from your RO/DI water is if the unit was not running right (highly unlikely).
Questions above are good and need to be answered to get to the bottom line. My question is your rock....did you use dry rock, and was it properly cured. Note, I'm not talking about the cycle, but the cure, where you allow the rock to sit in saltwater for however long it takes for the dead stuff within to totally decay and leach out. I've got a hunch that is where you high nitrates are coming from. I'd be doing 50 percent water changes every week until you get that number down.