If marking the IRA/SEP/SIMPLE box results in a change in your refund, the only reason is that somehow TurboTax believes that you have basis in nondeductible traditional IRA contributions and is preparing Form 8606 on which the taxable amount is being calculated as $0. Examine the IRA Information Worksheet. Otherwise, click the Continue button on the page that lists the 1099-Rs that you've entered and proceed to the page that asks for your basis in nondeductible traditional IRA contributions to see what's there.
However, if that was was the case, it seems that the taxable amount of the Roth conversion if entered by itself would be incorrect as well.
