There are two very different thrust curves for the AT N3300R floating around online. They have roughly the same net impulse, but the shapes of the curves are quite different in ways that make it difficult to predict launch rail velocity. I believe the source of the discrepancy is that the curve in the Tripoli test report doesn't match the curve in the AeroTech catalog. The test report shows an initial thrust around 800 lbs, level for most of the burn; the AT catalog depicts an initial thrust around 500 lbs, rising to over 900 lbs after ~2 seconds. That makes a huge difference when simulating the rail velocity for a heavy rocket.
I asked Karl Bauman at AT about the discrepancy in an email and he said: "I would use the curve depicted on the TMT motor testing report, it is within 1% of the value we obtained during motor testing."
That being the case, I based my RASP file submission on the data in the test report here: http://www.aerotech-rocketry.com/uploads/8b644cd4-9eb7-4eb4-a834-23590baca387_n3300r_tra_cert.pdf
This report also seems to better reflect real flight data.