I had one that did this. on mine it was absolutely the saucer switch, it took me forever to figure it out... I believe the way it works is the first time it goes through, it uses the switch above the saucer to know the ball went through, then just automatically kicks it out. On mine, the saucer switch itself didn't work. The first ball would go through and kick out, but when one was sitting in there, it would just sit and wouldn't kick out...
once I checked the switch, I noticed someone had tried to replace the diode on it... but had put it on in such a way that basically the switch was shorted... so I'm not sure if the software disables the switch or what, but check that diode (the reason mine was shorted was because they had rebuilt the switch stack with something in the wrong place, shorting both sides of the diode together)...