Hmmmm, the width issue seems strange to me. Especially since you said you reset the skin.
After inspecting your website, it seems as though you have a bunch of CSS stylesheets loading but none of them include the Thesis css.css stylesheet.
Becuause of this, the Thesis CSS Reset is not taking place. Is there any way you could add Flatisfy to a fresh WordPress install and check if the width settings work then?
The first image below shows the stylesheets that load with Flatisfy out-of-the-box and the second image shows the stylesheets loading with your website.