I don't think the software can correctly simulate a flight with cones or other short/fat rockets. I am limited to OpenRocket, and it cannot accurately sim dynamic stability - RockSim may have similar limitations.

The swing tests I have done seem to confirm the "Massless Cone" method of finding the in-flight stability of a squat rocket.

What I normally do is:

1: input the massless cone and find the dynamic (in flight) stability.
2: Remove the cone, and reduce the mass of the rocket to "0"
3: Make a mass item the same weight of the total rocket weight, and position it so the CG/CP relationship is the same as was with the massless cone attached.

Have fun.

__________________
John Adams
"There is a lot of rocketry under 20ns"