I made a small change that should eliminate both players getting put on the clock at the same time.
The problem I've experienced is not with players being put on the clock at the same time, but with the first player returning after leaving the server or leaving a wrong match, and inviting the second player who doesn't respond to the invite, therefore timing out the first player, who isn't recognized as making an invite by TourneyBot. Is this problem being addressed?
Law of Probability -The probability of being watched is directly proportional to the stupidity of your act. - from Lorenzís Law of Mechanical Repair