Duplicate Order/Items stay in cart

The past few days I have been having an occasional issue with customers checking out.

I see them go through the checkout process, I get an AIM debug email (success!) and they get an order email, but the items do not leave the cart.

In a few other instances, the customer has 2 charges against them for a single transaction.

The last and final instance I have seen was an order came through, but I saw nothing in regards to Authorize.Net payments, the CC #/exp date were blank and absolutely nothing was recorded on my CC processors site/transaction logs.

Changes that I have made in the days leading up to this is:

Installed 'Save for Later' mod.
Installed Newsletter/Mailchimp integration module.

Neither of these modules touch anything in the order.php file, but 'Save for Later' does touch tpl_shopping_cart_default.php

I am obviously thinking they are related, but I don't have a clue where to start investigating this issue.

Help!