Site broken when launched as iOS web app

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Is there any reason why my site would break horribly when saved to the home screen and launched as a web app? Is there any way to debug it?

It appears from the way it renders that all the HTML and CSS loads fine, but I suspect jQuery is not being loaded, as most of the positioning and sizing of elements is handled by scripts. However, that wouldn't make sense because there is a "loading curtain" that calls fadeOut() on window load, and on the web app that element doesn't even appear.

Unfortunately when trying to search for "ios web app jquery", all I get is people trying to figure out why their click events aren't working.

The site works fine in iOS 6 Safari. I don't think it's a caching issue as I've deleted and added it numerous times (clearing Safari cache as well).

Here's the link if you want to check it out: http://kanakado.rggwebdesigns.com/

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After debugging it with Safari web inspector, I found that it was using very old versions of the CSS and JS, so adding "?v=1" to the end of those files' src attribute forced it to fetch the latest files from the server.