At the very end of the clean function script tag nodes embedded in the nodes stored in the ret array are spliced into the ret array itself.

The clean function should not touch those scripts with a type different from "text/javascript" (e.g. custom types used for script island metadata). This check is partially in place, but still missing from:

ret.splice.apply(ret, [i + 1, 0].concat(jQuery.makeArray(ret[i].getElementsByTagName("script"))) );

The direct use of getElementsByTagName() causes all non-"text/javascript" script tags to be moved to direct children of fragment. If this is combined with temporary container nodes (e.g. the Blind effect in jQuery UI) this causes those script tags to be 'eaten'.

A simple fix is $.grep()-ing the result from getElementsByTagName and only retaining those script elements with the "text/javascript" type.