on the gcode tab, check the box that says "include m101/m102/m103" OR the 5D firmware box also produces extrusions. im not sure which one is applicable to you r printer. i run marlin firmware on mine and i do not have the m101 box checked but the 5d box is.
Are you using a profile from the S3D configuration assistant? You really shouldn't be having any of these issues unless you made a bunch of changes to a profile or tried to create one yourself. All of their built-in profiles wouldn't cause this problem.
I did not change anything with the default profit other than my speed, infill, and such parameters. So yes the built in profile is causing this. I included the m101/m102/m103 commands, and I was able to see the print in preview. However, I am still getting the same problem.
What profile did you select from S3D? None of the Prusa profiles that I have used had that option disabled, so I'm doubtful you were using a stock profile...