This is exactly what I meant by panel applets going out of order.
I have faced this issue too. This one, I can usually get around by sort of moving other applets (like moving the last one up if I cannot move the second last one down). I also had a look at panel.vala (conflict_swap and other functions) for anything that could cause this but they seem good to my (fairly inexperienced) eye.
Lastly, have been away from my machine for a week or so (kinda vacationing) so have not updated regarding what happened.