I have a Superchips Flashpaq 1815 tuner. I had it on my '04 since new up until I totalled the truck this past April.
I bought this '05 in May and I loaded the tuner on it.

I have been running the 87 octane performance tune. Today I (breifly) changed the tune to "stock with options". "With options" is a setting that means its stock but I can still adjust for gears, tires,tranny shift options, ect,ect.
It had been running a little odd so I wanted to see if the tune affected the issue.

WOW the truck did NOT like that at all. As soon as I started the engine it threw up codes:
P1000 monitor checks not complete
P060C internal control module main processor performance
P2106 Throttle actuator control system forced limited power
The engine went into fail safe mode.
I took it for a drive, and of course it drove like crap.

I stopped and reflashed it back to the 87 performance tune and now all codes are gone and its running fine again.
Except for the odd driveability issue I mentioned before.

Isn't that weird?
I dont think I'll run that (stock with options tune) again.

Must be a bad tune in my tuner?

 

Are you trying to run tunes on a 5.4 3 valve with an aftermarket intake? If they aren't custom tunes, it's running too lean.

 

No its all stock. Last night I flashed the truck back to stock and completely removed the tuner all together.

It runs great stock. Actually better than it did with the performance tunes.