Funny, I just had a similar thing happen to a player last night.
Player was in multiball, jackpot was lit, and he successfully shoots the ramp to claim the jackpot. Jackpot animation happens, but ball does not get diverted back to the lock properly, and game fails to award him points for the jackpot.
Not sure if it went back to single-ball play, since the game acts pretty similar to single ball play after you hit a jackpot and stay in multi-ball.
I had just fixed a similar issue on F-14. The upper diverter was failing intermittently. This meant that sometimes when you would hit the right saucer for "Release" or to collect the Fighter Jackpot, it would play the callouts for the appropriate award but not award multi-ball or jackpot points. This happens because the game doesn't award the points or multiball unless the ball is diverted to the proper saucer. Fixing the diverter solved this problem.
Anyways, because of what I learned on F-14, I took off the glass while he was still cradled up with both balls, and tried triggering the switch on the left ramp return just past the diverter and also placed one of his balls in the ball lock, thinking this might award those points. All this did was award him the lit "million" for hitting the upper right ramp, and kicked the ball back out of the lock.
I suspect the switch on the upper left ramp entrance may be flaky, since that is the only switch that would trigger the diverter from that shot. I've also experienced it diverting the ball to the left ramp return in the middle of a Tailslider round, which seems like it could be related as well.
I'll be at the location of my RAD! today working on various things and will report back if I find anything.
For the record, I'm running the tournament ROM that always awards 5m for jackpots.