I've read that using the "Separate Connected Surfaces" fixes this, the issue with that is when the model has a crap ton of these connection issues S3D "Stops Responding" for hours before it finally decides to do its thing.
splitting the surfaces is not an easy task, especially for meshes generated by meshmixer's support+object ..
there is much faster and better way to do it. you can export, from mexhmixer, object and supports as separate STL's, load that stl's into the s3d separately and manually position then so they are properly positioned one to another. It is rather simple to position them, double click on them and make sure "change position" (x, y and z offset) values are identical for both objects, if not manually set them to be identical ...
then you should create one process for the object and second process for the support and voila ..
what does not work if you do it this way is - there is no support as s3d is concerned so no dense layer, cannot setup system to print only dense (interface) layer with e.g. dissolvable filament while everything else is printed with normal filament... so you can ignore the "support" tab completely, but you can define infill percentage, shells etc etc .. for support structure seaprately from the object, assign different material to each of them etc etc... it works rather good!
here you can see prusa generating support in mesh mixer, exporting part and support as separate stl's and loading them in to slic3r ... you can do exactly the same thing with meshmixer + s3d
integrates with Simplify3D and allow you to
Calculate print time accurately (acceleration, max speed, junction deviation all taken into consideration)
Embed M117 codes into G-Code
Upload your G-Code directly to Octoprint
open source and unlicence