If it was a direct roll-over to a qualified IRA (meaning the money passed from one to the other without coming into your possession) 1099-R box 7 should have a distribution code (likely G). This needs to be entered in order to be recognized as a non-taxable roll-over. If you received the funds, then later put it into a qualified IRA you will need to seek the "Help" to guide your steps, also so this doesn't appear to be an excess contribution to an IRA.