f you are unable to get expected rates when using the Handling Matrix extension there are likely to be a number of reasons why this might happen. Shipping can be inherently complex, and setting up custom rules can result in missing/conflicting rules if you have not configured correctly, missed rates or misunderstood a concept.
Please firstly review the WebShopApps TroubleShooting Guide.
If issues remain then reduce the csv file back to the test setup and ensure you can get correct rates then. Slowly build it back up piece by piece to identify where the issue is.
Retrieve the logs from the extension, and review these to ensure the destination, shipping groups, weights, prices, etc match your understanding of the products.
If you do not believe that you are receiving the correct handling fees try using Flat Rate with an obvious rate, such as $10. That way, if you have a small increase you can see an obvious difference.