My site, http://www.bradbrownmagic.com, uses some scripts that rely on Jquery: Cufon and an image rotator. The code is placed in the Header Inserts section. They stopped working when I upgraded to the newer ATA version. The problem is that beginning with version 3.6.1, things were rearranged in the header. Now Jquery isn't loaded until after the Header Inserts.
The best solution I could come up with was to edit the ATA code so the inserts load after wp_head(). I assume there are situations where this could be a bad thing, or it wouldn't have been changed in ATA in the first place. However, this worked for my issue. Here's what I changed. In header.php, I moved the following line of code from higher up to right before the </head>:
<?php if( $bfa_ata['html_inserts_header'] != '' ) include 'bfa://html_inserts_header'; ?>