You're definitely not alone in this struggle. Payment reconciliation issues often occur because:

Amazon doesn't process payments order-by-order but in batches, combining multiple orders

Various deductions happen simultaneously (referral fees, FBA fees, refunds, etc.)

Timing differences exist between order completion and payment processing

Try using the "Date Range Reports" under Reports > Payments to see detailed breakdowns. The "Transaction View" is particularly helpful as it shows individual order IDs with their corresponding fees.

For easier reconciliation, export your payment reports to Excel and use pivot tables to group transactions by order ID. This will help you match payments to specific orders more accurately.

If you still have discrepancies, consider using third-party reconciliation tools like SellerLegend or A2X that are specifically designed to solve this common issue.