The difference was that I did not have the "allocate personal use items to Schedule A".  If I click that, the percentages in the Sch E expense lines change, but the 1098 info will only appear on either the Sch A or Sch E, depending on whether I've checked Main Home or Rental Activity on the 1098.  What I'm trying to do is have the 1098 in the return, and just allocate the appropriate portions of taxes and interest to the Sch A and Sch E. 

If I select Rental Activity on the 1098 and link the data to my rental's Sch E, the entire portion goes to the Sch E.  I can then enter 15% on the Sch E expense line and deduct just the applicable portion, but the balance is not showing on the Sch A.  If I select Main Home on the 1098, it all goes to the Sch A.  Isn't there some way for me to enter the data on the 1098 and direct the applicable portions to both schedules?