Yes. cPanel's buildapache script doesn't support Zend, eaccelerator, or ioncube, so you'll need to add these manually after the fact. Also, any php options that were previously compiled will have to be selected once again, because the script doesn't remember the previous config. You can run "php -m" via the command line to see what modules are currently compiled into php, or you can make a phpinfo page:
<?php phpinfo(); ?>
<?php phpinfo(); ?>