What does your data look like? It sounds like File A and File B may be dissimilar. You may need to name the fields the same which hold the same data or to map them to each other.
Thanks for the reply Carl. Indeed the two files are dissimilar although both have the pertinent data to plot the polygons (Longitude, Latitude, Point Order and Polygon ID). While the field names aren't exactly the same, I did edit the relationships so that they would be properly identified. It still didn't work unfortunately.
Let me know if you think of something else I might try.