It is my understanding that the Override System should work for the following module file structure:

includes
modules
Your Template
I have added the following files structure:

includes
modules
Your Template
pages
popup_image > jscript_main.php
However, the original system file still functions. Also, as a test, if I rename the original file jscript_main.php to jscript_main.old the popup window fails even though I have added the additional override file structure.

All the other Override System structures I have used work fine.

Sawhorse
(below are the particulars of my site)