[Mark Padgett]

In running clock games, the clock runs during free throws (except, perhaps, in the last two minutes or so, depending on your rules), so if they foul, then request and are granted a timeout, when they come out of the timeout to shoot the free throws, the clock starts again. That's because once the timeout is over, the clock starts when the ball becomes live. This is different than in a stop clock game.

Seems to me that you guys just need to straighten out your rules and this problem might go away.