An idea about bug that could have happen, just a wild guess:
Maybe all missions that are triggered by arrival to an area is bugged?
Has anyone recently done a mission where something happened when you arrived at an area?
(Someone I met said he couldn't finish "find waterholes" mission or arrival to the Goki wave area, noone dies when entering middle island - does anyone even get the warning message?), and hunt aetherex on the hills doesn't currently work.
Wave events seems to work, but (just curious) do you get a count-up for the "Kill daikiba" for daikibas killed there? (Now I mean the specific "kill daikiba in bulls pen" area mission, not some general hunting mission like the iron mission or "kill'em'all").
Next time anyone of you, who hasn't done the vaccine missions, pops by the middle island, can you just check if you get some kind of warning message, or if nothing at all happens when getting ashore there.