I faced the "Upgrade" button on the kiosk for the first time myself this past week. Usually, I am cleared in advance, but on this occasion I was waitlisted. When I checked in at the kiosk I wasn't sure if that button was intended for those who had not yet requested an upgrade or not.
I was actually afraid that by checking it, it would put a time stamp on my upgrade request that obliterated the one placed on the record when I had originally requested the upgrade days prior. Nonetheless, I selected it.
Based on your story, it sounds like the "Upgrade" button at the kiosk actually means, for those already on a waitlist, "Activate me on the airport Upgrade Standby List." Seems like Delta needs to make a better distinction on this one, because I truly was confused when confronted with it for the first time.
One would think that the natural default here would be to simply activate on checkin anybody who had already gone to the trouble to get put on a waitlist in the first place, rather than force the individual to make another affirmative request for the upgrade.