I had the same thing a week ago. Driving with cruise control on, no reason I could see, tripped the check engine light, told me to service the throttle controller and went into limp in mode. Took the off ramp was, doing some weird stuff. Shut the truck down and restarted it and it wasn't in limp in mode anymore but the check engine light stayed on. Ran but it just wasn't right. Wasn't in limp in mode but low on power. Pulled out the Pedal Commander thinking maybe it was that. Shut it down later for several hours and called the dealer. Seemed to run fine with no Pedal Commander and the check engine light went out by the time I got there and the dealer said it was fine. Got it home, put it back in, threw the check engine light again, pulled it out again and the light went out after a couple starts. So that tells me it WAS the Pedal Commander.
Emailed Nick at Got Exhaust and he told me some things to do and told me to clean the mass air flow etc etc. Been scared to plug it in and use it again. The reason it scares me is that I travel a lot for work and don't like the idea of being stranded in the middle of nowhere. It just worries me... might try it again this weekend. Not really sure what I should do but I did everything Nick suggested and I couldn't see any signs of dirt of buildup. I mean the trucks just got 35k miles and about 30k of those are highway so it's not like it runs a rough life.
SIDE NOTE... I never use ECO mode. I have a V6 so no Pedal Commander is pretty much ECO Mode. It always ran in City +2 and I never changed it.