Hi Jeff,
I'm guessing the doors are currently in a single wall set to 'All relevant stories' and 'Projected' stretching through both stories .
The trouble is that doors and windows, when set to symbolic, will display on any storey they intersect ignoring the Floor Plan Cut Plane, while D&Ws set to projected will only display when cut by the FPCP. Both of which occur in your situation.
I can think of three options to try.
You could try splitting the wall into two at the level of the top of the window. Set the lower wall (with its door set to symbolic) to display on 'Home storey only', and set the upper wall 'symbolic' on its 'home storey only' also. Unfortunately this may mess up any other windows you may have in the same wall, so you might split the wall lower down, leaving the door poking up, and place an empty opening set to overhead in the upper wall in the same place.
Another option may be to raise the FPCP on the upper storey so it is higher than the doors, and set the door to projected. This rarely looks as good, and will also mess with any other cutplane sensitive objects.
The third option would be to simply cover it with a patch, and move on with your life!
It's a shame there isn't the option like you get in normal library parts where there is a variety of 'show on storey' options to choose from.
Hope that helps.