PHPR is removing my custom javascript

I need to use database values for a custom field. I have figured out how to add a custom field to a page, and how to process the value afterwards, however now I need to assign a value to a javascript variable on pageload for use on the page.
On an ADD page, I have added a custom code snippet to before the header in the visual designer. The custom code snippet is as follows:
global $data;

echo '<script type="text/javascript" src="include/my_ajax.js"></script>';

echo '<script type="text/javascript">

var myact='.$data['fkActivities']+$data['fkActivityOverrides'].';

</script>';
However when I view the resulting ADD page, and look at the source code, it only contains this:
<script type="text/javascript" src="include/my_ajax.js"></script>0;

</script>
Where did the opening javascript tag go? Why is this?
Is there a better way to assign variables to javascript at the beginning of the page for later use?