That is an interesting question because it regards intuition of use.
I think the biggest issue is that you have the Joomla banner at the top, followed by the navigation buttons. I see the SGDK banner and automatically I assume that content is relevant to SGDK where the other content (at the top of the page including the buttons) belongs to Joomla.
I think you should replace the Joomla banner with the SGDK banner, then remove the SGDK banner below the buttons. That should make the buttons stand out better.
Perhaps the style of the buttons add to the effect. They are light like the background. Maybe make them darker. Again, this is an intuitive thing and there could be a better way to do this.
Another thing may be to have two buttons, one "home" button, and a second "projects home" button in the template. Clicking the banner would have been more intuitive it was at the top instead of under the Joomla banner, so creating an extra button may not be necessary.
At first glance I actually expected there to be a text link (regular blue hyperlink) in the text of one of the articles that would take me to the files. In fact I went to the second page looking for this. Perhaps you can just put one inline with the text and it will probably solve the problem without changing anything else.
Chris