Just in case there's people around still having this kind of issue, this is what fixed it for me.
Go to your "process settings" (with "Show Advanced" enabled) -> then "Other" -> check the "Dimensional Adjustments" settings.
That needs to be set to 0.00 mm. In my case it was set to 0.50 mm and that's exactly the error I was having, about 1mm of error all around the models.
Of course you may want to set it to just to a lower value (like 0.05 or 0.01) but that's what fixed it for me.
Enjoy and thanks to the Simplify3D staff for the awesome software