1) In Polaris I typically beat the boss first since I used sun serpent and occasionally it doesn't kill the minions. After I am finished with battles the boss reappears.
2) At random times when I'm casting there is some sort of invisible ward. Typically after I've used an accuracy ward, the next turn when I cast it'll act as if there's another.
1) When you say reappears, do you mean in battle, or after the battle is over? I seem to recall a mention of a boss reappearing after a battle if killed first, but you don't have to battle the boss again unless you want to try for more loot.
2) Could you list the gear you are using (hat/robe/shoes/wand only)? I've had this happen before in the past myself but only when wearing certain gear, namely gear from the Road Warrior's pack.
If I had to guess for the second one, it may have been that way probably since the second half of Empyrea came out. I'm not exactly sure, but that's my guess
If it's post (or around the time of) Empyrea part 2, I was not active. Little late to noticing that, and it was just starting after I came back from a year off. Thanks for clearing that up