Ok, so there were two issues, one quest became "squelched", no idea why or what for but they don't issue updates if the do. I couldn't tell why it happened in some cases and not in others so i just commented out the code that did it.
Second issue is a bit more serious, when you go back from new context to game context (when you're not using jump), all displayable from the new context are destroyed... there is no way around that which I can see so you should never update the quest right before the end of a label in new context (or just use jump).
In either case, it seems to be working a bit better now.