Description:
If you have  a .shp file where the projection definition is stored only in a .prj file, Spotfire 7.13 and lower cannot use it to draw the map in the defined projection system.
Symptoms:
After loading the .shp file and changing the reference coordinate system in the map chart layer to match the .prj projection definition, an error similar to the following is reported.
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Reference System Mismatch (Map Layer)
'Map Layer' can only be shown in the coordinate reference system 'EPSG:3857'
Change coordinate reference system
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Where the 'Map Layer' and 'EPSG:3857' depends on your analysis.

Cause:
Spotfire 7.13 and lower does not read .prj files and needs to have the projection definition stored in the .shp file itself.

Spotfire cannot use a shape file with a .prj file for the projection.

Update Spotfire to 7.14 or higher or use a GIS tool to merge the .prj information into the .shp file. See the Reference section below for examples on how this can be done.

http://webhelp.esri.com/arcgisdesktop/9.2/index.cfm?topicname=defining_a_shapefile%27s_coordinate_system