I’m not aware of any change to magnificPopup, but we do plan to remove it soon so I would recommend moving to the documented DModal API.
One thing which has changed recently is the way we load JQuery. It now becomes available slightly later in the boot process. So, window.JQuery may not be available until after Discourse has booted.
You can make your script run after boot by switching <script> for a Discourse ‘plugin initializer’:
<script type="text/discourse-plugin" version="0.8">