Thank you for the Bolles information. I would imagine the relationship finder looks for the shortest route and if the shortest route includes John Warren, it is going to use that and ignore ones that have a valid gateway as it's source.
I did, this afternoon, do some research on John Warren and found nothing that would confirm that he is connected to Royalty or the Barons. Certainly, the Warrennes are royalty ,but as of now, there is nothing that I can find, that connects John Warren, [1585, Nayland, Suffolk Eng.], to the Barons.
As the NEHGR 64:355 says, John Warren's line goes John  1) Elizabeth Scarlett, 2.) Rose 3.) Rose Riddlesdale; John  1.) ? 2.) Agnes (or Anne) Howlet, 3.) Margaret Firmett; Robert  Margaret; _______ (father of the foregoing Robert and a Thomas). It is probable that this line of Warrens intersects with a Royal line, but it has not been determined as of yet, as far as I am aware.
In the line presented on WT, there is no "gateway plaque" on John Warren-238...only a PGM. The next three generations follow what I found in the NEHGR. Funny thing is, that in one generation (from 3-4) the Warrens go from living on the East coast of England all the way to outside of Liverpool. Also the information becomes more royal and full. The name changes to Warenne, in generation 4, from John Warren, immigrant, which is plausible, but I can not find a Wiston, Nayland, Suffolk, England on a map. Going further back, all the Warrens are from near Liverpool.
Is there anyway that a profile can be flagged NOT to be included in a relationship calculation...or can you run more than one relationship path? I seriously think it is going to take some serious inquiry to find out how, and if, John Warren's (and Dr. Joseph and Dr. John Warren, both famous doctors during the Revolution and were Warren's G GSs) line extends to the Baron's.
Thanks again for your input