Is the check engine light on the dash illuminated? If it is, there is/are code(s).
For Chrysler vehicle, the scanner has an option to check powertrain or drivetrain. As, they were a transmission shop, they probably scanned your drivetrain (transmission), instead of the powertrain (engine) computer. If they did say that they could not communicate with the engine computer, that is something that you have, probably a Chrysler dealer, to have a look at.