Nil found the solution to this problem, but I'll post on it
I simply took my old cds reloaded EQ and moved the zone files from the original to the emulator (only the ones that gave me problems and only one zone at a time)... I never had any problems with the mobs showing up correctly after that.
Any kind people out there know where I can find some good db's... I know they take a lot of work so I won't be suprised if I don't get any replies. Main concern is zone in points and working portals.