I might have misunderstood what you were saying. You said that when you put the two together you were showing a lower income. That was not possible: two W2s will show more income (instead of $3000, you will have $4000). As far as why adding the other W2 (with $1000) is affecting your refund, that depends. If no tax was withheld from that W2, and depending on your other income, it is possible that your tax refund is lowered by that much. In this public forum we don't have access to your tax return to know for sure.
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