gvSIG-Desktop 1.9. User manual
If you mark the “Use spatial index” check box, a spatial index will be created which makes the layer loaded in the view appear more quickly. This is because the view is loaded using this index.
If there are write permissions, a .qix file is created with the same name as the layer it is associated with in the layer’s original directory. If there are no write permissions, the file will be created in the user’s temporary file directory.