Chris:
The simplest way to handle Walls is to confirm that they are set to the current story (Geometry and Positioning > Home Story) and they are Symbolic (Floor Plan and Section > Floor Plan Display > Show on Stories: Home Story Only and Floor Plan Display: Symbolic). This way they will be placed on the current story, and ignore the Floor Plan Cut Plane (FPCP) which allows for the walls to appear on multiple stories but increases the complexity of their display options.
You should add a Signature to your Profile (click the Profile button near the top of this page) with your ArchiCAD version and operating system (see mine for an example) for more accurate help in this forum.
David