That was going to be my guess! The default setting for Configuration->Affiliate Settings->Allow Self Commissions is false.
Snap Affiliates' commission-calculation happens one time ... when the order was placed. Use the Customers->Referrers tool and, when you "Pay" an affiliate you'll have the opportunity to conditionally-select and/or modify the commission-payment amount for each order.
I'll write up a GitHub issue on that; thanks for the report.
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