A new wrinkle on that song (to mix my metaphor ):

1. Flying domestically A-B-C-D. Had previously applied for a mileage upgrade using 15K miles. A-B and C-D clear immediately, B-C is waitlisted. Do OLCI successfully, but get "We are unable to print your boarding passes; please see agent/kiosk." Go to My Itineraries. I see that B-C has cleared, but My Itins is showing two entries, one confirmed in F and one confirmed in Y. Go back and cancel check-in. Still can't check in with an upgraded B-C leg. So I call, explain the problem, ask them to clean up the PNR, removing the entry for the Y segment. She does so.

2. Go back to OLCI; this time it shows all three segments upgraded correctly. Check in and try to print boarding passes -- "Unable to print boarding passes; please try again later or see agent/kiosk." Logout and go back to OLCI where it shows checked in for all three upgraded legs. Try to re-print boarding passes; get same error.