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OK, so I had a problem with this theme disabling the javascript functions within Drupal, specifically the collapsible fieldsets in the administration>settings page. This, after much hair-pulling was due to the rather dumb fact that I was using a window.onlad call in my custom javascript that powers the theme. After Searching drupal.org extensively, I finally found this which pretty much sums it up. Simply change any window.onload calls to:

if (isJsEnabled()) {
addLoadEvent(yourCustomJSFunction);
}

I have now excountered the situation where I somehow disabled the drupal javascript inclusion in the head of my document. I fixed it by adding a call to drupal_add_js() in my template.php (where I should be calling my JS from anyways I have also learned :)).