I reduced my property taxes to the percentage of Principal Residence Exemption (P.R.E.)/Qualified Agricultural exemption, but still received the message the property taxes were reduced for credit. Why were they reduced further?

Verify you have subtracted the school operating taxes levied on the non-P.R.E./Qualified Agricultural portion of your parcel.  To compute the taxes which can be claimed for credit, exclude the school operating tax and multiply the balance by the percentage allowed by the local taxing authority.