Similar situation last month. SYD-SIN-MUC on SQ and LH. Both in premium economy and the 15 hour SIN-MUC flight on LH was upgraded at ~ T-72 into business using PlusPoints. I was only credited for the first segment as both tickets numbers were the same, and had to call and mess around for more than 30 minutes to get it fixed. To cap it all, for 22 hours flying I got an absolutely miserly 500 PQP for SQ and 750 PQP for the LH flight. Partner earning on non 016 stock, which is needed to use the PP upgrades, as a joke and needs to be fixed.