Unity opens a second blank window and has "Hold on" window

Every time I open unity it opens a second instance of the editor that interferes quite a bit with what I am doing. On top of that everytime that I update a little bit of code unity opens up the “Hold On” asset refresh window for about 15-20 seconds. Unity also has been throwing random errors that are related to the editor and a sometimes just strange other things happen. I have tried completely uninstalling unity and reinstalling even so far as to wipe it from roaming and temp folders and the registry.

Here is the photo of the second screen:

@ZeCopyCat had this question but nobody ever answer it.

This can sometimes happen when your layout settings are corrupted. You can try from the top menu Window → Layout → Revert Factory Settings.