I made the changes in header.php. Changing the order the files load in seemed to do the trick for me, <?php wp_head(); ?> is usually loaded at the bottom of header.php, but I found it worked when it loaded just after where I load jQuery.
Guess we are not getting an answer, but I fixed my issue. I just changed the order in which plugin scripts are loaded. I just moved <?php wp_head(); ?> just underneath where I loaded my jQuery. Now it works again.