Loaded a save world from a previous version, quests not complete and I cannot complete the very first checkmark quest: Welcome to All the Mods 6 Sky. I thought the quests I have already done would still be completed.

Thank you.

Read the changelog before you update...
And to fix the cannot complete quests bug, delete the contents of [saves]/<world>/ftbquests. This will reset quest progress if there's anything that wasn't reset though