Make sure your skin is set to GravityCustom at the Site level and then also double check the actual site page settings you are on to confirm it is also using GravityCustom.
If you have it set to GravityCustom it should not be pulling the CSS from any other skin except that folder and I think portal.css is still shared across all skins.
Just as a test you could empty the contents of your skin.css in GravityCustom do a refresh in your browser and see if the design gets all goofed up. Maybe you made your edits to the wrong css file?