I am having this problem too,   I can't do any quests above the first or second level.   Takes out a major fun part of the game for me.   I am also using a custom sov\kingdom.

Ah. I think I know what is the issue? The custom empire was created using 0.93, and I just reuse it straight after I patch it to 0.95?

Can this be a possible cause? I am sure the game is the right version cuz I still get Town, Conclave, Fortress, etc.

Made a new faction and new sovereign and have the same problem now that i was brave enough once to go for one. Won't work.

All quests are available at start, you don't unlock them. I don't know what happened in your game thiotes. Try deleting all created factions and sovereigns, then reinstall maybe.