The error that occurred was a result of using two different releases of the gun (I reviewed several in-progress protoypes during the review).
We realized that one version we had was driving the screws just a hair deeper than the other, but the cumulative result was that the boards were 1-1/2" out of square at the end of the deck.
The boys now have strict instructions to pull measurements every several courses to ensure everything is straight and running even. If you run your boards wild, it's a good idea to use a spacer at the ends of the boards to prevent a bow from forming in the decking.
Also, the guns seem to need a breaking in period because now we really aren't jamming as frequently.