If I'm remembering correctly, a second switch needs to be activated to award the points and advance the sequence. If there isn't another loop switch associated with it underneath the other stuff, I'd suggest checking to see if the right inlane switch is properly registering, as that may be the "last" switch the machine needs to register that the loop was properly shot/made.

Bolstering this theory is the fact that I've had the ball miss the inlane on the way down and had the sequence broken.

Try checking that switch for proper operation.