The transfer would not count as a contribution. I'm just not sure how that amount is getting into TurboTax. If you contributed to Company A and that is on your W2 and then contributed an additional amount to Company B and that is on your W2. Where is the transfer amount showing up? A rollover contribution should show in Box 4 of your 5498 and not be included in Box 1,2, or 3.
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