The exceptions raised about accessing the registry may be due to a lack of permissions. Do you have an Administrator account on your Windows PC or just a User account? If this is the case you can’t install new programs on your system and must see with your system administrator.
Otherwise the first issue you describe seems to indicate that you are using a perspective that was corrupted; did you try to do “Window >> Perspective >> Reset Perspective...”?
By the way, how did you install System Workbench for STM32? Did you download the installer or did you install maually in a pre-existing Eclipse installation?