It's possible the changes in your refund total are influenced by more than your SEP contribution. Was this reported on Form W-2? That's where the known issue arose, but that has been resolved.
You might compare your 1040 each time you change the SEP contribution and check where the changes are made. If you're using TurboTax Online, you can see your 1040 following these instructions: How do I preview my 1040? In TurboTax for Desktop, use Forms Mode.
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