I replied via email too, but making it public:
Yes I'm pretty sure I know the problem - if the containing div for the hype animation (that is, the one from wordpress) does not have a width or height set, then that will effectively be seen as zero. The 100% width/height of the hype animation then will be 100% of 0, which is 0, and the document will be hidden.
I don't know much about the genesis theme, but you'll need to make sure that the container either has a size or a percentage. If the container uses percentages generally then you also need parent containers to define themselves in a percent or a size at some point otherwise the same problem will happen.
Alternatively our general recommendation is to not use flexible sizes with wordpress, but it sounds like you specifically want to do this for your content.