are you locking the first ball via the shelter or the left ramp? Sounds switch related to me. the subway lock has only one switch on the up kicker, the other ball just sort of rests by the side when locked. I think there's a switch further up the subway which detects ball entry. if that's not working correctly it won't know what ball is where.

I am in Leicester. get yourself on pinballinfo or ukpinball as there's people in Blackpool who may help.

Hitting the ramp and then the captive ball does not give me a lock at the saucer. It does light an institute zone which if then complete would light the 2nd lock at the ramp. Quick 2 ball multiball is only available as an award from the shelter. So I'd say that what you're seeing is the start of regular 3 ball multiball. Maybe this is a feature of the code you're running or a setting?
Mind you, I'm running proto3 software.

try setting:
adjustment #40 to resets
adjustment #48 to fast
adjustment #43 to 1st lock