Using a version of Table Rate Shipping equal to or greater than 3.0.11 and now price based shipping is using the tax inclusive price of products to calculate shipping rates? That is expected behavior and was a bug fix from an earlier version. However, in some instances, perhaps you want to calculate the shipping on the tax exclusive prices. This can be done with the following code snippet:
Not sure what to do with code snippets? See What Do I Do With These Code Snippets?