If you ever have an issue with the way simplify3d is slicing try to do the following which was recommended on reddit:
The way to fix this is to add 0.001mm to the primary layer height. i.e if you are using 0.2000mm, change it to 0.2001 and so on.
S3D has some weird bug where it can't always detect vertices properly, or something like that. I believe that the official line from the devs is that the model has problems, but that is BS.