Just an update...this happened again, and I checked the fault code myself. P16F3 which is suposed to be "internal control module redundant memory performance malfunction"
I found this TSB: http://www.dixie-electric.com/tsb/TSB_171.pdf
The first time around, dealer said there was no code logged, and no CEL when they started it. (I call BS.) This time (even though it's past warranty) I'm going to print out this info and make a copy of the report from the first time and go to a different dealer. Hopefully they'll fix it, because the TSB was published before I even bought the car so I feel like they should have caught it the first time, and since they didn't they should fix it now.