We are the one building template for our friend's site www.cvtreasures.com and we didn't remove the $messageStack from our template because no beneficial purpose of doing that.
Upon further checking we realized that we used FEC (checkout) module in this site, and the related file is actually tpl_checkout_stacked.php
In this file I didn't see the standard zencart's $messageStack which are below:
So I put that codes into this file (mod), not sure if this proper because I dont really inspect this mod deeper and how they work.
<?php if ($messageStack->size('redemptions') > 0) echo $messageStack->output('redemptions'); ?>
<?php if ($messageStack->size('checkout') > 0) echo $messageStack->output('checkout'); ?>
<?php if ($messageStack->size('checkout_payment') > 0) echo $messageStack->output('checkout_payment'); ?>
My conclusion that this issue has something to do with the mod it self, probably we can post in their support thread later for clarification
Perhaps you have other opinion?