Allocating a retirement distribution over 3 years in TT

After going through the questions and determining the distribution is able to be allocated over 3 years, the federal tax due box changes to reflect the lower distribution for year 1.  the following screen asks whether you want it all allocated to the current year and if so, check the box.  I did not check the box but clicked on continue and the 3 year allocation changed back to all in the current year and the tax due increased to reflect that.  When I go to the forms tab and choose the 1099 retirement form I see that the box that asks if it is all a qualified distribution is blank, even though I answered yes to that in the interview questions. If I check this box it does the 3 year allocation.  I am concerned that I am forcing a calculation rather than having TT calculate it correctly and if my forcing it will allow everything to flow through the returns properly.  Can someone help please?