As it is now, if a ball becomes trapped after it is ejected from the trough, but before it hits the shooter switch, the game will ball search. This is primarily for older games where the ball could get caught on the lip of the trough release point. The vibration from the ball search could fix it.
You are right that the timer begins to count immediately. But it will pause as soon as the shooter is seen though. See the test "!switch_poll_logical(MACHINE_SHOOTER_SWITCH)" in common/search.c. Make sure you have marked your shooter switch as "shooter" in the md file otherwise this won't happen. This matches the behavior of real WPC software, which will ball search if the shooter switch is not working.
Brian