Did you say you rolled it over?  Even if you put it back into the same account.  If they took out any withholding did you also replace the withholding?  Otherwise the withholding is a taxable distribution.

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 below.

Be sure you indicate first that you "...moved the money to another retirement account (or returned it to the same retirement account)."  and the you "rolled over all of this money to another IRA or other retirement account (or returned it to the same account)."

The only way that I can get the screen to which you refer to appear is by unchecking the IRA/SEP/SIMPLE box.  If that box is checked it will not ask the question what did you do with the distribution.  In my case I have an inherited IRA which I received but then reimbursed in entirety (including the withheld taxes) to the same Bene IRA.  I have deleted and reentered the 1099, checked the box that an RMD was not required (and also tried checking the box that it was).  I have reimported and tried those answers as well.  The only way I can get to the screen asking what was done with the funds is by unchecking the IRA/SEP/SIMPLE box.