If your ROM is version 3 or higher, you don't need to time out AI because of this common I&S problem.
EDIT: OK, I see you said start didn't release. Leaving this info in case it helps someone else out.
http://www.sternpinball.com/downloads/sppROMreadme.txt
- Added player-abort feature for Alien Invasion. If a ball becomes
hopelessly stuck (e.g. 2 balls sneak behind the I&S drop targets), then
the player may hold in the start button for one second. This will kick
out ALL currently locked balls with no effect on the stage or the
ballsaver. The player may then try again to lock all of the balls for
that stage. It is recommended to abort the current stage as soon as a
ball is trapped because no ballsaver will come on when kicking out the
balls.