Hi,
I am having a similar issue trying to create a pop-up page for a file resource in Moodle 2.4; it instead creates a separate pop-up to a window that describes the resource with a link to the pop-up page for the file at the bottom of the description. So one gets two pop-ups instead of just one, not what I want. I happen to also have an install of Moodle 2.4+ and the problem doesn't happen in that Moodle, it has been resolved. So, you might encourage your admin to upgrade to 2.4+ to see if that solves this problem for you.