If you create a zone, put a web part in it and then delete this zone, you can still see zone with the same ID but in the gray box. You can remove it by adding zone with the same ID to the layout or removing the web part.

You may want to check the following settings:

1. Make sure the "Show for document types" property value is empty and the "Document types" property is set to appropriate document type, such as "cms.news" (without double quotes).
2. Make sure the "Transformation" value is set.
3. If you specified any "Path" property value, set it to /% and test if it helps. If so, you may need to adjust the property value.
4. If you specified any "Site name" or "Culture code" value, try to clear the values.
5. If you specified any "Maximum nesting level" value, try to set it to -1.
6. If you specified any "WHERE condition" value, try to clear it.
7. Make sure the "Check permissions" value is set to false or - if you want to check the permissions - make sure that the current user has appropriate permissions.