Were these flights on CP or AC metal? It seems that if you were on AC metal, it often shows up as J, but my experience on CP metal earler this week, and posted on the weekend, is that it shows as R on both the boarding pass and the account statement, and only gets the 100%, and not the class of service bonus that AC gives for coupon upgrades. Last month I had a BA boarding pass ex-LHR on a CP flight number (CP metal) and it showed J on the pass but ended up R on the account statement with no change in the 100% points credit. It was an upgrade as well.
I'll be curious to hear how it posted, so let us know.