I have all the same issues as OP mentioned besides the Soul Jar one. I really hope it gets fixed in their next big patch they are talking about because I can't leave the island unless I want to fail all those quests. I'm guessing some of these might have other quests or consequences later in the game too.
I think they do have consequences. Pretty minor, but it still sucks.
Spoilers for Act 2, Tribe of Saheila and its subsequent quest:
Already went to the elves, but it never gave me the option to give back Saheila's amulet. Also, when I rescued her from the Lone Wolves, one of the dialog choices was something like "*Ask how she knows who you - who is she?*.
Err...because we already met in Fort Joy? Unless the Saheila in Driftwood is some twin...
Although there was a choice in Tribe of Saheila where you say you were the one who rescued Amyro(IIRC), so I guess the game knows even if the Journal failed it? But then that wouldn't explain why Saheila doesn't know who you are.
