Here's an update. It's the plugin you are using that is breaking the layout. Once I disabled the plugin, the layout structure was fine, then I activated once again, sure enough it broke the page structure. Now the really hard part is to figure out what is in the plugin that is causing it to break.
There is one thing that is conflicting with css such as:
This exists in the theme plus this plugin, so one is causing layout issues. The plugin one should be renamed with a prefix, but this has to be done by the developer. Many themes use #content in their css layout.
There might be a problem also with the fact this theme is based on the Bootstrap framework which is a responsive grid. So the plugin's templates may also be causing the problem with the layout...which I think is the real problem.
In the end, I don't think this plugin and this theme are 100% compatible without doing some recoding for this plugin's portfolio template because of how they were created. Unfortunately this plugin adds two portfolio files to the main theme's folder among the other theme files and it loads the header and footer and sidebar as well (this is part of the conflict) for its layout. Now if it was just the content part only, then it might be ok.