Just to check we are on the same page, there is no "override", you just type in the percentage, right?

You are using ProSeries, right?

Can you post some screenshots of your Schedule E Worksheet (be sure any private information is not  posted).  That may help us to figure out what is going on.

Oh wait ... did you enter any personal days?  That may be what is going on.  You should enter 365 rental and zero personal days (assuming it was rented all year).  Even if it was not rented all year, you need to enter zero personal days, but then manually calculate the proper percentages.