I had this exact same issue a month or so ago. I kept getting different stories from AS regarding the upgrade since I was on AA ticket stock. I just kept calling back every day until I found a nice guy who did not look closely enough at the ticket info and just confirmed (not waitlisted...but confirmed)the upgrade for me. (well either he did not look closely enough or he just did not care and wanted to take care of the MVPG).

Funny thing was that it was a mileage ticket booked through one of my credit card points programs. The company Chase uses for mileage redemption bought the ticket on AA but AS thought it was a paid reservation because on my boarding pass it printed out the cost of the ticket, $286 something. I guess when the reservation gets "transferred" in a sense to AS the mileage redemption gets lost in translation and it ends up being some normal fare class (I forget which one). I even ended up EARNING AS miles on the travel
See this thread for more info.

sorry to go off on the random tangent there...but I think its a pretty cool glitch!