At around the 1-2 minute mark(of the in game timer),every
room in the house becomes identical.Usually they all become
the bedroom.Never,except at the very beginning,is there any
story taking place either.I can still randomly catch bad
guys(after 1 minute they can't be seen anymore,but the
sensitivity meter will flash red every so often,along with
the beep noises).I've tried all emu settings(latest
version).Any help?Iso file loads,cue doesn't.

It's most likely a problem with your image. I've played a lot of Night Trap lately, and I've never seen those problems.

never got those problems either although my version is in french for some reason