Found: %pass quest paid the rewards through its own shortcut, which skipped the step that hands over the next quest in the chain.
Fix: %pass quest now finishes a quest the same way a normal completion does, so the follow-up quest is granted straight away. This is in the next RF Online 4.55 update.
To verify: Use %pass quest on a quest that leads into another, such as a class starter quest: the rewards arrive and the next quest appears in the quest log.