I was playing around with JBM Ballistics today and I think I might have figured out how to do this.
You have to use the "Trajectory" program to do this.
First you have to run a simulation with the conditions when you zero the rifle. In the results window it should show an elevation in MOA. Make a note of this. Then go back to the entry window and enter the Elevation number and go to the bottom and uncheck the "Elevation Correction for zero range" box.
Now, in the fields that have to do with atmospheric conditions, check the box labeled "Std. Atmosphere at Altitude" and enter the DA in the altitude box. The program looks like it uses the pressure and temperature for standard altitude, which I think is what Density Altitude is.
I haven't totally proved to myself that it's giving me the right information yet but it looks promising.