Purely as an exercise for the purposes of illustrating why there is no issue, try unticking Coast at End on the Extruder tab of your settings. Then take another look at the simulation. Now the explanation...S3D shows a simulated extrusion whenever the nozzle is extruding. Where the nozzle is not ext...
The bottom image, the gcode simulation, shows a simulation of what the gcode generated by the slicer...so if it shows three extrusions, the the gcode has the instructions to print three extrusions. Your top picture shows what your printer has done with the said gcode instructions. Either the nozzle ...
This has been as issue for a very long time......back to even before S3D was written! Its a Windows thing....S3D is probably not hanging - but displaying at a location on the desktop outside the area a single monitor does not show. And if you can't see it, you can't use it!...and the "blame&quo...
In the same folder as the saved default factory file ( see the linked thread for the folder name ) there will probably be loads of gcode files from recent prints. Zap all of them and the software should load faster.
This happens when you have the parts too close together on the bed. There needs to be some distance between parts otherwise the sequential printing will treat the close parts as one.
Looking at the photo of your machine, you have room to move two of the parts away from the third...