Let me start by saying I am no programmer, but I can look at code and get an idea of how it functions. Writing custom code is beyond my skill set though.
That being said, I was looking at how this theme seems to dynamically generate a new div class="ajax_slide twelve units" blah blah blah div each time you select the plus button to view the next item in the portfolio. This got me thinking. If you can dynamically create the div why not just dynamically destroy it when you move to the next slide using something like the jQuary .remove() method - http://api.jquery.com/remove/ - or something similar?
I know for a fact that destroying the div that is play an iframed video will stop that video from continuing to play. This seems like a simply solution for an issue that, as I found out, plagues a lot of other themes as well as this one.