Hello,
Each of those boxes is a menu module that you have published to the bottom row, they will always be published there whether responsive is enabled or not.
You have some kind of plugin enabled that is modifying css:
http://dol49csaak3y7.cloudfront.net/media/plg_jchoptimizeThat will need to be disabled as it is altering core css files. It's manipulating it so much that it's applying this css to those modules:
.s5_light_modules .module_round_box, #s5_component_wrap {
background: #fff none repeat scroll 0 0;
border: 1px solid #d8d8d8;
padding: 15px;
}
But those modules are not called inside of "s5_light_modules" anywhere in the source so it should not be applying. They are called inside of "s5_dark_modules" in the source. So either the plugin is causing the issue or something has been modified in elsewhere in the core files. So the first step will be completely disabling that plugin and if you'd made any modifications you'll need to revert them.
Another thing you can do is remove the following from the css above, which should be in template.css, but your plugin is calling a different css file:
background: #fff none repeat scroll 0 0;
border: 1px solid #d8d8d8;