The situation when Magento Order Amount differs from Amazon Order Amount happens due to the next settings:
1. In Account Settings -> Order Tax Settings -> Tax Source is set to:
- "Amazon&Magento" - Magento Orders use tax settings from Amazon Listing. If there are no tax settings set on Amazon, Magento tax settings are used.
- "Magento" – Magento Order uses Magento tax settings.
2. Magento Tax Rate is set according to Customer Tax Class and Product Tax Class.
3. Tax Rate corresponds to the particular region.
For example, If a buyer is from USA, CA and for CA tax rate is set to10%, 10% will be added to the price in Magento order. So, the price of Magento Order will be more than price of Amazon Order.