Two identical quads, one doesn't get off the ground

Tickle me this, Ardupilot people.

I have two quadcopters. Same hardware. I have the same scripts running through Mission Planner for both. One gets off the ground, but the other doesn’t. Why?

They both connect to their mission planners, they both work fine in manual mode, but when set in script mode, you can hear the differences between the two quads and can easily tell that one does not have nearly as high of a PWM value as it should. The scripts are identical so this should not be the problem. None of the motors are dead, the ESC’s are calibrated on each quad. Hardware works and they have completely identical setup. They also have different Net ID values so they do not interfere.

This is mostly an open forum for troubleshooting so sorry if I put it in the wrong category.