Has Anyone Encountered An Issue???

I am going with a study abroad group in May, first to Taipei, then to Shanghai for 3 days and then back to the U.S. I have confirmed that my trip qualifies for the waiver and I have a confirmed seat on a flight to the US. However, I'm wondering what happens if I try to get on the flight from Taiwan and they won't let me on the plane!? Also, does anyone know whether it takes longer to get through customs under the waiver policy than with a visa?