Well, it would seem that there is something wrong with the teensy code. Or, maybe there are multiple USARTs brought out and you're not connected to the right one. I think I would start looking at that first. I can see a scenario where they would use a secondary port for the scanner and leave a primary port for the console connection.
You're probably going to have to tear into the teensy code and see what it is actually doing.
You have an advantage: You know the scanner works with the Arduino so the issue isn't with the scanner. Half the battle is over!