Interesting thing I saw today logging onto cowtool. I flew FCO-MUC-YYZ in August, flex fare. First leg on LH, TATL leg on AC. I got 50% SQM for LH leg and 100% for AC leg as expected. Today, cowtool seems to believe I should have only gotten 50% SQM for the AC leg, even though it's a flex fare. Supposedly because it's fare class L? Doesn't really make sense. Also, not that it matters to me but the United PQP earnings shows as "???" as if it can't calculate that. Not too sure about that.
As for the return leg of the trip started in August, it still shows I should earn SQD according to the original fare I purchased (latitude) but 100% SQM. Recently, I moved the flight to a couple days earlier and changed the fare to flex, paying a fare surcharge. So now both SQM and SQD don't line up for this return leg.