Script trigger points are basically totally broken if you turn on invincibility and then do something you wouldn't normally be able to do. Sorry!
Without knowing exactly what you've done I can't really help, but a good thing to try would be to travel to the ship from the teleporter at the end of the first space station level, talk to violet, then travel all the way to vitellary through the second space station level! This might reset a few things, though...