OK, so I have submitted a ticket to them on my issue and have found out why we are having the issue that we do. Here is the ticket text I supplied encase it might help you guys.
There is an issue with using the ress=1 in the short code. As soon as it is added the slides no longer appear.
<?php echo do_shortcode( '[SlideDeck2 id=229 ress=1]' ); ?>
Works fine with
<?php echo do_shortcode( '[SlideDeck2 id=229]' ); ?>
Ah, so I have tracked down the issue, when using the ress=1 it doesn't display the slides because we have the admin area set to require https://, but not the front. If you view the front via https it works fine, but when viewing it via http it does not.
We do not have a valid SSL assigned to this site right now, so can't say for sure that a valid SSL would fix the problem. A valid SSL isn't in the plan for this site as it's functions do not require it, but still want to use the encryption for the admin area to secure our log in credentials.