Might the problem simply be the following:
We expect PF3 to make us descend in time to reach a certain waypoint at the altitude that is set in the Adjust ... flight plan page - and that is how it should work. But I have the impression that PF3 sometimes waits for us to reach that waypoint before it clears us to that altitude. So in Martins example he couldn't reach RESMA at 15000 ft. but was told to descent to 15000 ( with a step at 24000 because of the large interval) when reaching RESMA.
That would also match the experience I had in the flight I posted above.
And it would explain why some flights are going fine: if the waypoints are close to each other with only 2000 or 3000 ft between them, this problem would be barely noticeable whereas it is a severe problem with waypoints far away from each other.
If this is the case a workaround would be to shift all target altitudes one waypoint up.
Just a shot in the dark but maybe worth a try.
Ralf