I would suggest re-checking all the connections, especially the ground. If that doesn't work, perhaps you should order the bypass plug for $10 and send your box in to get checked out.
I've had a similar issue with my truck, but it was only while running the Bully Dog Triple Dog version 2. 0. 4 on the performance or extreme settings.
Truck runs perfect with the TST and the newer 2. 2. 2 software on the BDDL.