Is it possible the skills past the last checkpoint are not practiced if you click on strengthen skills. Today all skills past the last checkpoint became 4 out of 5 while all above stayed 5 out of 5.
This would be a little annoying because it takes a while to do them all individually, especially since i'm done and want to keep the tree golden.....
It's possible that skills don't turn golden very quickly, especially if you haven't practised that specific skill/the words in that skill a lot recently. I think it only starts getting suspicious if skills don't move towards golden after multiple 'strengthen skills' practice rounds.
BTW if I'm not mistaken passing a checkpoint using the checkpoint test gives an extra 'strengthening' bonus to the practice level of the skills before that checkpoint. It could be that by doing the checkpoint tests you have strengthened these skills more than you realise, causing a difference with the skills after the last checkpoint.