meshmixer.ini (now with fresh default settings)as well as the autosave directory is created automatically if it is missing. It's ok. By default MM does an autosave each minute until there are ten autosaves. After that it overwrites the oldest one.
Also the pop up if you press Space is ok. That's the Hotbox giving quick access to certain rendering settings.
If you can't see the bunny or sphere or any other imported object in the 3D viewer I think it's related to your graphics card . Is the viewer black totally or does it show some strange black to grey gradient?
If there are more than one graphics devices (e.g. an onboard chipset + a decent graphics card) make sure that MM uses the better device.
Next is to make sure that you're using the latest driver available for your graphics device.
To ease the work of the graphics device:
Next if you're on MM 3.3: Disable AntiAliasedRendering in Preferences>General. Shut down and restart MM.
Last, worst option: Enable EnableBasicRendering in Preferences>General. Shut down and restart MM.