Justin,
Have not used Hagen ammonia, nitrite or nitrate kits, but you shouldn't be reading any ammonia or nitrite if the LR was cured.
Are you using dechlorinated tapwater for water changes? If so, this could account for ammonia and nitrite levels.
Do you have an aragonite sandbed, or crushed coral? Aragonite is a better sandbed. It allows microfauna to live more easily in it, whereas crushed coral is considered by many to be a detritus trap with very little microfauna which will fuel the growth of unwanted algae and cyanobacteria.
One last thing.... was at AI this morning checking out the LR. They must have gotten a large shipment lately because the LR tank was absolutely full
Was looking closely at the rock and noticed most of it had all kinds of dead stuff and various algae all over it. I thought if I were to buy some, I would scrub off each rock before putting in my curing tank. Did you scrub off dead material before putting the rock in your tank? If not, this would also be another source of nutrients to fuel cyanobacteria growth.