I completed all the relevant nodes for the initial clears but was still almost 1100 short of the full points total.
Checked through and made sure I had cleared each node 3 times, which I had. A second check through identified that despite 2 nodes having been cleared three times, they were still worth full points.
Cleared them again, got the remaining reward and green and points halved. I was traveling at the time, so it could be a glitch, but the points and rewards are normally inseparable.
