The IRA/SEP/SIMPLE box is not supposed to be checked because it was not a distribution from an IRA.... It is 401(k) withdrawal, that you rolled into an IRA. After you enter(ed) the 1099-R, there is a page that asks "What Did You Do With The Money From [Retirement Plan]"? Be sure you indicate that you "rolled over all of this money to an IRA or other retirement account (or returned it to the same account)."
Answering these questions correctly will result in your distribution showing up as non-taxable.
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