Perhaps the Cd that Rocksim is calculating is a bit conservative? I can get 1600 feet (from a 6K ASL launch) with a manual Cd input of 0.48. It's possible the thrust profile in the ENG file for the C6-7 is a bit off, too. I know the D12 and E9 profiles in the Apogee-supplied ENG files are WAY off.
As a real-world example, I got a predicted altitude of about 635 feet (on an A6-4) for an 18mm competition model I flew a couple of years back. The actual altitude was tracked to 734 feet. I think Rocksim had been over-cautious on the calculated Cd. Of course, the actual motor could have been 'hotter' than the ENG profile for the A6-4, as well.
All-in-all, Rocksim is great at putting you "in the ballpark", but real world scenarios can vary from simulations substantially.