I have just setup a new website with Joomla! and VirtueMart. The problem was that no matter what I did USPS shipping was $0.00. After several hrs of troubleshooting and reading these forums I finally found the problem. The account I was using had the correct zip code, but was showing the wrong state. This was causing the USPS shipping module to receive a "Wrong Country" error and show shipping as $0.00. The problem is that the transaction would continue as if nothing was wrong, no error messages, allowing clients to have $0 shipping charges.
BTW, I am using Community Builder if it matters.