Hi Armando,

We troubleshot this issue and found that strange negative decimal numbers entered in the Sale Price and Wholesale Price fields which were new fields recently added and would have a "null" value which may be what is causing the miscalculation of the Totals and Prices so we recommended  running a SQL Statement for those 2 fields and change the values to "0" . When a transaction is processed the Product ID along with many other fields are saved to the data table, having such large, negative invalid values in the fields below could throw off the Cart from recording or saving the correct data with a transaction which in turn can cause wrong information to be passed to wrong places. 

We also recommended an upgrade It is quite possible the upgrade solved the issue however this is still being investigated. If you have any orders go through incorrectly please let us know. It makes it very difficult to determine where or what is causing the information to be recorded incorrectly since the issue cannot be replicated on your site, or we can't recreate the issue on the test portal so the issue may be something with your cart install possibly something with your cart install has gotten out of the sync.

Thanks,