I had some issues with a script tag not loading inside a panel. The panel was set to only be visible when a view scope variable was set.
It turns out that this is by design for HTML5.
When script tags are inserted into a document using Ajax/innerHTML, the spec states that the script tag should not execute.
"...script elements inserted using innerHTML do not execute when they are inserted..."
My workaround for this was to set full refresh for the event that refreshed the panel.