If your windows simply disappear into thin air, it might be Spaces at work.
But in order for this bug to occur, you need to have had:
- Enabled Spaces
- Assigned applications to a space other than space 1
- Disabled Spaces
With spaces off, it seems something triggers the window manager to still move the windows to the now offscreen spaces and thus, windows are gone.
If this happens, use the Spaces dock icon to open up Spaces preferences, enable spaces and you’ll find your windows.