From the way I understand it that is not all that uncommon of a situation. Each airport and TSA operation are somewhat of an independent entity. They have to follow general rules and practices but they can use measures outside of the norm (eg. no jumpseating without a boarding pass or uniform). Heard of the some of the same similar responses too such as "your airline doesn't operate here" thereby making you a non-operating crew member. In some cases these guys are just doing there jobs and all they know to look for is where is the boarding pass.