The Donation Form part is a "dynamic" part that will maintain all parts used in the main page, and display them on the custom confirmation.  If the main Donation Form contains other parts, these will also appear on the custom confirmation, causing it to appear incorrect or improperly formatted.

To work around this, you could use a separate Payment Part, which can be selected in the Donation Form setup.  By using a Payment Part, you would be using an entirely separate page, allowing the custom confirmation to appear separately from the Donation Form.