I think the issue you are facing is most probably due to the booking classes. Although you say that these were never stated anywhere my experience is that they're visible when booking on the TAP web site and they're also given in the 'Electronic ticket - passenger itinerary receipt' that you should have received (it's one of 3 emails that TAP seems to send following any booking).

Regarding you upgraded return segment, I imagine this booked into P which earns nothing with M&M, I fell foul of this myself earlier in the year. Tried to recredit to A3 where it should have been worth something but was rejected by them too - still waiting for a reply to my follow up.