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I must confess I have never heard of it happening in that way. Can you send it back to Jody for testing. The only thing I can think of that is remotely possible is your body sent a static charge and it scrambled the program in the PCM. I suppose another option is that the chip is somehow wired different but again, that is reaching. When inserting the chip I always remove the PCM harness and PCM and connect it then reinsert it. I also always make sure I am grounded but that is just because I am **** about it after having shocked one PCM because I was lazy and didn't want to disconnect it or take the key out.
To be on the safe side I would send the chip back to Diane and Jody so they can at least look at the files and make sure they are the correct ones for your truck and that the chip is working correctly. I personally hate the whole PATS thing.. I guess its a good for preventing theft but it also can cause really screwed up no-start issues even without a Tuner... I know this from personal experience! anyway its really easy to shut the whole system off all togather. its just one setting change in each tune. then to get rid of the blinking light you just unplug the PATS module under the dash... Just unplugging without disabling the system in the PCM will not allow you to start the truck... I have more info from AE on the PATS system. PM me with an email if you want to see that info...
The plus side is u don't need to buy $35 replacement keys and if you have only one key you don't have to go to the dealer for programming the second key..
To be on the safe side I would send the chip back to Diane and Jody so they can at least look at the files and make sure they are the correct ones for your truck and that the chip is working correctly.
I don't think that wrong programs can screw up the base programming on the PCM, do you? He took it out and it still ran poorly till it was reflashed by the dealer. The chip overrides the base program in the PCM and should not affect it once removed. That it affects it even after removal and is fine after the base program is reflashed should indicate that the base program itself has been corrupted.
The dealer also had to reflash my keys, because the truck wasn't recognizing them
Sounds like something wiped the entire base program. I am not sure but give Jody a call. He might be able to test the unit out. Somehow, I can't see it doing that so I suspect a burst of static electricity when installing. Weak theory but maybe Jody has a better idea. Give him a shout.