This is actually a very confusing topic for most Amazon sellers, and an excellent question!
The reason for this is Fetcher applies a fully adjusted sales calculation, while Seller Central only captures total product charges.
To see that base sales figure, just expand your Sales widget on the dashboard and look at the top line as seen here:
The 1099K includes all charges to buyers (i.e. shipping concessions, gift wrap services, etc.). Even if you did not really get the funds, for example, gift wrap services ordered on FBA orders – or FBA shipping the buyer paid – this is included in the gross revenue reported on the 1099K.
Fees and other expenses are not deducted from the reported amount on your 1099K. You are required to keep these to deduct your costs from the gross revenue reported as being collected from buyers for your orders. Refunds are not factored in either - that would be considered a deduction.
Think of it like a W-2 from an employer. This shows what the company paid you before any withholdings. The difference is a W-2 provides these deductions; a 1099K does not.
The best way to reconcile the numbers is to run a Payments Transaction Report on Amazon. You can find that here: Seller Central Transactional report
Once there, click the ‘Generate a report’ button. In the pop-up, choose ‘Summary’, set your custom date range, then click ‘Generate’.
When the report is done, you can download it as a PDF. This will include all FBA and FBM orders and should match the 1099-K gross sales numbers.
This report will also show all the Amazon related deductions (i.e. gift wrap, shipping, etc.) that is apart of the 1099-K gross revenue numbers. These are your deductions needing to be reported.
Then you can include your own deductions, like travel expenses, product acquisition costs, shipping and office supplies, credit interest payments, equipment, etc. (monies we paid outside of Amazon to run our business).
With these 3 pieces of information; 1) 1099K, 2) Amazon payment summary, and 3) your total expenses outside of Amazon, you should have everything you need to provide to your tax preparer.
I know this is a confusing topic, so please let us know if you need any further help!