It could be as simple as an update that needs to happen. It's not unheard if for a custom tune to get written and a stratigy number get mixed up or software to look at something different because it needs to be updated. ALOT of us have used SCT products for sometime now, and very few issues have ever came up and I can't recall a one that warranted a trip to the stealership. It's usually something simple, do you have a copy of your stock tune saved someplace off the SCT device? If so I would move the tunes off, update and load your stock file and only that file to the tuner and try that.
2007 CC, Lariat, 6.0L, TreadWright guard dogs, straight piped out the back, egr delete, blue spring, 6.4 banjo bolts, high idle mod(bcp), bulletproofed, SCT Livewire TS with Drews street runner(under development for high elevation), Innovative, and Vivian's tunes, ww2.