What coil are you using?
BTW, when you originally changed timing for the orange box, how much did you have to change it from the MSD setting? It would be no surprise at all for there to be timing differences, based on circuitry differences. They could easily have different internal delays or even trigger off opposite edges of the pickup pulse.
Any way that you could have flipped the polarity of the pickup connector on the distributor when you installed the orange box or the new box?