its already booked and has been for months. Its a reservation that includes a SEA to MKE flight. I just noticed this a couple weeks ago so hopefully its a Skywest glitch and not a bigger issue

The only thing I can think of is that it was originally booked in Y on that segment until they figured out the U space bugs for the skywest flights then when U came available I upfared to the gold U space along with me and a companion.
See my post about my upgraded flights. You might check the confirmation email you got when you upfared and upgraded to make certain that it shows you in class U and not in your original booking class. Note: The My Trips itinerary showed me in U even when the confirmation email did not. So it was the email that indicated the problem in my case.