The additional geometry is really things like coplanar faces--removing the uneeded edge dividing them, and stray edges--depending on the settings you have made for Cleanup3. It's good to use the tool as you model before you create too many extra edges etc, and avoid modeling that does so. SketchUp doesn't make the extra edges, though plugins might (such as SandBox).
I would turn off the CleanUp purge functions and do the purges in the Model Info window. See if that helps.
I find CleanUp3 to be so slow as to be unusable in larger models in v2019, regardless of the cleanup job or selection. It is often faster to cleanup the model on my own. It seemed to work fine in 2016. I've never tried 2017.
Haven't heard of multiple instances of the application opening.