Hey thats some good advise, I never thought to disconnect the battery! Makes sense. Getting my unit custom tuned next monday..can't wait! Having the CAI and exhaust done already was one of the reasons I chose this route, also having the fuel I always run in the truck while tuning it and of course seeing my truck on the dyno!It could be one, both, or none. Has it been recurring or just a 1 time event? Have you tried disconnecting the battery for about 10 minutes to allow the computer to refresh with the new tune and intake? I have always disconnected the battery to clear the computer after installing anything aftermarket. Is your canned tune compatible with your intake? I would start by calling the tune maker and ask the question about compatibility with your chosen intake.
Others on here know way more than I do about this truck, so hopefully they chime in.