Last game the 4 of us where left:

player1 flagged for 2nd
player2 flagged for 3rd
player3 flagged for 3rd and
player4 unflagged.

territories: player2>player1>player3>player4
and player 4 was killed.

Automatic end of the game and:
1st: player2
2nd: player1
3rd: player3

So player2 placed higher then player1 though he (actually it was me:)) had a lower flag...

Bug or something I didn't understand? :)