I've done the same thing you describe and never had that particular glitch -- but, I have had problems with upgraded AS segments when checking in with both the AA agents (at MIA and AA*/EWR) and the CO agents at EWR.

So I don't think your glitch had to do with the types/method of upgrades requested, but with the poor systems integration between carriers and poor training of the OA agents checking in the AS flights.

Edited to add: My problems weren't with collecting certs, but with the computer insisting I present a paper ticket coupon on an eticket itin, and AA being unable, in both MIA and EWR, to print BPs for my connecting segments on AS, leaving me not checked in for the AS connecting flight and at risk of having my seat given away on short connections at ORD and BOS. I would love to hear from Missy or anyone else at AS whether there has been improvement in AA's ability to print AS BPs.