So I followed the questline in Astryl's and got to this:

[x] Find Elder Orynn
[x] Gather Plankwood Logs (5/5)
[x] Gather Rope (10/10)
[x] Gather Village Supplies (1/1)
[x] Defeat Elementals (20/20)
[x] Investigate Shrine (1/1)
[x] Collect Elemental Cores (10/10)
[x] Defeat Vorpar (1/1)
[ ] Return to Ethernia

But returning to the castle/different places doesn't complete it? Is there a special way to this or am I too low in reputation?

Same in the orchard, I'm stuck on

[x] Talk to Myrida

and it doesn't dissappear?

No need to worry, it's just because the newest quests haven't been released yet. When the new zone (not the mega-zone) is released, you should be able to go to the castle to complete the last quest.

Myrida is the last quest in the orchard, you've done everything there. The list doesn't go away when all the quests are completed, it stays there.