I'm also experiencing this problem, I think.
It occurred when I was doing the "Cornett's Call" quest. I had previously retrieved the Conch from the Old City before accepting the quest from Dereo. I got the other conch from Takano's villa via convincing him with the religion option to give the conch freely.
I didn't get jumped in Neketaka by the thief that usually confronts the party after you get the conch from Takano's villa.
I've traveled the breadth of Neketaka several times, but I haven't received any random encounter after I did that quest.
EDIT/UPDATE:
I managed to trigger 2-3 random encounters in Neketaka. I'm not sure what did the trick, but I completed all of the RDC/VTC quests up to Crookspur before the random encounters popped up.