In the screenshots below, you can see where there are fine details in the model that do not get printed in S3D whereas Cura sees them with no issue. Is there a way I can fix this in S3D? Thanks for the help!
Stab in the dark on the basis that a dark blue print in the simulation indicates single extrusion wall printing....and that such details are usually added using separate shapes.....
Try using the "Separate Connected Surfaces" option on the Mesh menu. If you get one or more extra items in the model list after using the option.....then the slicing will work better!