kim_w, I did some research and found the theme files. You know these commercial theme files use non standard ways to implement particular tasks because there are limitation with the provided official APIs.
I checked and found that your Agent Theme is using the_content_limit function included in the functions.php. And calling the_content instead of the_excerpt within the customized function. That caused my Hana Flv Plugin to produce output for the case of content output, not the excerpt output. That's why you got all the scripts .
Just to make things clear , my plug-in works OK with the themes using standard the_excerpt function. Yours is having problem since it's not using the standard API.
Since this is custom modification, I would not update or modify my plug-in but rather you should check your theme file.
In functions.php, add below lines after line 310
global $wp_current_filter;
array_push($wp_current_filter,'get_the_excerpt');

Also, if that line number does not work, just find the 'the_content_limit' within the functions.php file and add the above lines after that.