the clocking is quite random...i guess while under heavy load botthreads may get suspended multiple times per turn wich leads to bots having far less than a second per move. my final submission has timeout checks all over the place but it seems like even an assignment sometimes takes more than a few hundred milliseconds.
50% of my losses are timeouts while winning (interestingly...if my bot is loosing anyways he rarely times out)
at least im not the only one with this problem:
http://ai-contest.com/visualizer.php?game_id=9346272