My auto setup continues to tell me to switch my surrounds with my fronts. It is telling me my fronts are small and my rears are large. What am I doing wrong?

Adjust your crossover points before you run the auto setup - the default of 100Hz is on the high side, and if you dial them down a bit the test tones won't get confused. You might also make sure to elevate the microphone to approximately ear level if you haven't already.

I have my mains at 60, my center at 80, and my surrounds at 100. Are you saying I should set the crossover to 80 for the test on the surrounds.

Yes, turn down the crossover on the surrounds before running auto setup. You can turn it back up later if you like, but try using 80Hz or even 60Hz during the setup.