Umm.
sounds like you are doing something really weird or just not using the right extrusion temperatures.

What settings are you using ?
ie:
bed temp
extruder temp
print speed

And are you using pla and abs at the same time in different nozzles ?

Also are you using the latest version of simplify 3d ? version 3.0 Because the flashforge profiles are weird. So far I haven't got it to print anything from version 3. So I'm still using the last version of 2. because I've got that down to a fine art.

They really didn't need to bugger up the profiles the way they did.