I don't know if this is the best way to report to you any bugs we found, but here I am. First I should mention we are using other mods: Thorium, tremor mod remastered, and some other smaller ones. So it could always be some arcane crazy interaction with those.
The simple bug was this: my friend got an easy clue scroll with the quest to plant an acorn. He was not able to complete it on my server, and he was not able to complete it in a single player world.
The other bug is this: I was able to complete quests on my server when no one joined. Once the other players joined none of us were able to complete quests. I had a Defeat the King Slime quest, someone else had place a dirt block quest, and I forget the other quests. I was not able to complete the Defeat the King Slime quest even after everyone left. And restarting the server with only me joining did not let me complete the quest. Only on starting a singleplayer world let me complete it. After that I started the server again and everyone was able to complete quests without issue (aside from the acorn one). Subsequent Defeat the King Slime quests have been completed several times. All this took place over the past 12 hours so I think there was no patch in the middle. What I don't know is if this is two different bugs combined or just one big bug.
Regardless this is a great mod.