Won't follow unknown links while I'm here at work.
If you visually see a difference, this is a rendering issue, which may or may not be fixed in a PHP script, but relates directly to the output source.
If the code is identical, and the physical servers have changed, my first guess would be the use of short tags is randomly scattered. Since PHP uses <? and ?>, if short tags are not enabled (they are enabled by default), then HTML will render <? . . . ?> as an output element in your HTML source which will often break the visual layout. Short echo prior to 5.4 is also affected by this directive, so if you have <?= then it will not echo with short tags disabled (unless you are on 5.4+).
So take a look through the HTML source and do a search for <?. Does it have any matches popping up? If so, then either convert those to use <?php (<?= would be <?php echo), or enable the short_open_tags directive in the php.ini or .htaccess.
If you are not moving physical servers (seeing subdomains here), then I'd put my money on a broken CSS link.