I have no influence on how FreeCAD exports to .STL. This also happens with several .STL-find that can be found on thingiverse created by OpenSCAD with this kind of issue. As every other Slicer handles these files witgout any problems I think an expensive program like Simplify3D should also do or have an (auto-) repair function.
So has this issue ever been resolved. I have had the same problem but only on my Kossel Mini profile. My reprap profile never does it and except for the machine dimensions and bed shape, the profiles are the same. sometimes it is just one layer and other times the whole hole is gone.
This is really sad. Even repaired files may have this issue and free programs do not suffer from this problem. Even if this should be related to the file which I do not believe the software should be as much intelligent as free programs. All other programs like Slic3r, Cura, Mattercontrol and KiSSlicer can handle this only the paid software fails. That makes me really really sad.
I had a similar issue with one of 4 holes getting partially closed in slicing only on simplify3d and not in replicatorg. I ended up rotating the model on the Z axis randomly until it had all the holes opened. Saved that to disk, and it now prints fine.