Hi Thomas,
I am new to Map Suite Desktop also so I'm not an expert. I do know that Map Suite Desktop (MSD) doesn't know anything about prj files. In order for shapefiles in different coordinate systems to display property together you must know in advance what EPSG number goes with each of your shapefiles and the EPSG number that represents the coordinate system in which they should be displayed. You do so as follows:
ShapeFileFeatureLayer railsLayer = new ShapeFileFeatureLayer(@"C:\CR\railways.shp");
Proj4Projection proj4Projection = new Proj4Projection();
proj4Projection.InternalProjectionParametersString = Proj4Projection.GetEpsgParametersString(4326);
proj4Projection.ExternalProjectionParametersString = Proj4Projection.GetEpsgParametersString(2163);
railsLayer.FeatureSource.Projection = proj4Projection;
This example assumes that the shapefiles is in geographic coordinate system EPSG 4326 (WGS84, its 'internal' projection) and will be displayed in EPSG 2163 (
US National Atlas Equal Area).
It's a bit of an inconvenience, but not too hard to work around.
Steve