That's another interesting family tradition that I hadn't heard before. One other researcher seems to feel that Samuel was from the Isle of Wight!
In considering the Isle of Wight theory, I looked in the current British phone book for Flakes and found a lot of them concentrated in the mainland area just by the Isle of Wight.
My branch of the family [William Jordan Flake] had always said that "Samuel the Immigrant" was "Scotch-Irish," which should refer to Scots relocated to Ulster.I found a few Flakes in Ireland, but none at all in Scotland.
I would be interested to see if you could find any sign of the Flakes in Wales in your research.