To learn more about projection files and how RAS Mapper uses  spatial reference systems, go here.

Sometimes a spatial projection file (*.prj) will produce the following warning in RAS Mapper.

The warning message is also displayed in the Coordinate Reference System of the RAS Mapper Options window as shown below. 

One common cause of this error is a field AUTHORITY["X",Y]. The field is usually at the end of the projection file as in the example below

To avoid the warning message, edit the projection file in a text editor and remove the AUTHORITY field as shown below

Then set the projection file again in RAS Mapper as the warning message should disappear (see figure below).