What version do you have loaded in the game?

If the game detects a problem with the Stewie playfield it will disable it. Check your setting to see if it is enabled. You may have to disable then re-enable also. This happened once at Marvins when the ball somehow got out and I had to do something like the above...but can't remember exactly.

There's an opto sensor at the drain part of the Stewie pf. If the ball isn't directly over it, it won't be recognized. Once in a blue moon, when I owned fgy, the ball would get caught just a fraction of a butthair on the guide before hitting the sensor. Have a look at that and/or check the opto sensor pin connectors.