Did you ever get it resolved? I have exactly the same issue on a flight I took last week: check-in upgrade reticketed in U and it has logged in activity as zero miles. Emailed AA who says "We need to look into this a bit more. We have escalated your request for review. Typically, there is a resolution within 30 days."

I'm wondering if this is a consequence of BA moving to new ticketing system. I have another upcoming flight in a couple of weeks where I paid for a promo upgrade and it has re-ticketed in U class, so I am expecting the same issue.