Problem: A layer with the same name as another layer is not used in an analysis
If there is more than one layer in the table of contents (TOC) with the same name, Spatial Analyst will use the first layer added to ArcMap to perform an analysis, regardless of the layer you select as input to a function.
ArcGIS 8.1 does not recognize the difference between different layers that have the same name.
Solution or Workaround
Make sure each layer in the TOC has a unique name.