Looks like encounters are still bugged under 1.02 (Prem/LE). If you keep the ball alive long enough in the bonus round (until the timer runs out), the game gets confused and you replay "Protect the child" again.
Easiest way to reproduce:
1) Start new game
2) Shoot left ramp to light encounter
3) Shoot left ramp again to start the first encounter
4) Complete all 3 levels and keep the ball active on the mini playfield until the timer runs out
5) Flippers will go dead, encounter complete animation plays and ball released back to the playfield. Encounter 2 insert is now lit.
6) Shoot left ramp again and you're replaying the first encounter "Protect the child".
The inserts on the mini playfield during this also go blue while the replay of the encounter is active.
I still think the base points on encounters need to be increased slightly to make it a more viable scoring path. Boosting the bonus level points in v1.02 is OK since we miss out on bonus levels 1 and 2 - but overall encounters are not worth it point wise as it's entirely possible to fail a bonus level without a single shot (ball deflects down the middle of the mini playfield on the final shot to complete level 3).