I am getting <? for all instances of where I expect the PHP to be.

[eluser]PhilTem[/eluser]
It is most likely a configuration issue of your webserver. Some configurations allow using

Code:

<?= $meta_title ?>

to automatically echo the succeeding variable, some environments require you to write

Code:

<?php echo $meta_title; ?>

Plus: Is your fileextension .php or anything else? If it's not .php it will not be parsed by the PHP interpreter thus the command <?= is unknown. However, you should not be having any other fileextension but .php when working with CI (except .htaccess)