You may need to adjust the taxability on your shipping and postage charges as each tax jurisdiction has different rules on whether or not tax needs to be applied to shipping and postage that you bill to your customer. Additionally, you may also want to adjust the income accounts assigned to these and to discounts. This can be adjusted in the Management Module.
Go to Management Module > Global Settings > Pricing Settings > Order Fee Settings.
In this area, you can set the taxability on both Shipping and Postage, as well as the assigned income accounts for Discounts, Shipping, and Postage.