When I got my 5 inspected this year, I just went through a whole ordeal because the mechanic's reader would not communicate with my car. It was extra weird because my bluetooth reader would work, and the shop's Snap On reader worked, but not the shop's Emissions reader. Also Emmisions read fine last year.
The mechanic theorized that one of the pins in my OBD port got pushed in and was not making a good connection. He ended up taking apart the dash in that area, pulled out the connector, and found that one of the wires had pushed out of the back of the port. He shoved it back in and then he was able to get a reading with the Emmisions OBD scanner. He recommended that I replace the port or try to re-pin that connection for next year, but I haven't attempted to do that yet.
I'm wondering if you have a similar issue where a wire came loose on the back of the connector?