Form 5498 is an information return.  It is not used to report information on your tax return.  There is no "roll over within 60 Days input box".  After you enter(ed) the 1099-R, there is a page that asks "What Did You Do With The Money From [Retirement Plan]"? See Screen Shot #1 below.

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)." See Screen Shot #2 below.

This is how you indicate that you did a rollover within 60 days.  Answering these questions correctly will result in your distribution showing up as non-taxable.