Sorry to hear that. That really stinks, but I am not surprised. These guys are a money-making concern more than anything else.
Since no one else can see your tax return, we have no idea how you think you shorted yourself thousands of dollars. This is a do-it-yourself tax software program, so if you made errors in the the way you entered your information, that is not the software's fault. Have you filed the return yet? Why do you think your refund is "short"? If you can explain then we may be able to help you understand and/or help you with how to amend to correct the errors.
You'd have to describe your issue before anyone could weigh-in on that.
Simply put, TTX can only guarantee their tax calculations, it can't know in any way if you missed entering some important information that you should have put in, but didn't.
IF you paid for LIVE support, then you should again contact a TTX agent, the same way you did so before you filed your tax returns, and explain the issue to get some help in preparing and mailing in an amended tax return (IF it really is something you need to amend in order to correct the problem)