OK, so we now have two confirmed areas that the trainer should be disabled. The Lot192 and 2nd Test subject areas.
update: only disable option 3 for the Lot192 mission and see post 15 for the Test subject problem.
[Edited by SL4T, 9/8/2007 10:31:21 AM]
The first time I seeded the entire area with proximity mines after the first Little Sister was killed at the 1st test subject. I did this before going and getting a second Little Sister. This might have screwed something up by killing splicers as soon as they spawned. Second time through I just killed them with the rocket launcher and shotgun when they got within range.
The Trainer basically prevents the thugs from appearing and attacking while the little sister extracts ADAM from the 2nd test subject. And this causes the script not to move forward.
So this is what I did:
The Trainer was enabled from the start of the level. Once the little sister started extracting ADAM from the 2nd test subject, no thugs appeared.....and it went on for 15 minutes.
So I made a manual save right there, exited the game, switched the trainer off.
I started the game from where I saved, and immediately the thugs attacked. so I quickly paused the game, started the trainer and resumed the cheats normally.
So you see, the trainer doesn't permanently damage any saved games.
When the script stops....save game....exit game....close trainer....start game.....wait for thugs to appear...start trainer.
other than that I never encountered any script problems during the whole game since I made sure option 3 was disabled during the Lot192 mission.