I took my truck to AutoZone, where they do a free code check for CEL (Check Engine Light). Their reader worked fine, so I went to a different inspection station and they were able to connect just fine, I passed with no problems.
Turns out the first place I went had been having lots of Fords fail and eventually realized it was their machine that was the problem....not before it flagged every one of them to the state as failing the emissions inspection. You'd think they would have gotten a clue a little quicker. I even asked if they had tried on more than one machine. Moral of the story - don't trust just one person/shop to do your work, especially if it has $ implications.