This year I am filing married separately and last year I filed married jointly, does this play a factor at all?
No. Stimulus payments are not taxable. The reason your refund decreased is because prior to entering the amount of stimulus you received, your refund included the Recovery Rebate Credit (as if you had not received the stimulus payment. Since you already received it, your refund decreased. The "recovery rebate" tax credit and stimulus checks are two parts of the same thing. The way the law is written, both the first ($1,200) and second ($600) stimulus checks were simply advance payments of the credit.
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