Patrick, I don't think there is any factual support for your theory regarding why there never was an Amateur at NGLA during CBM's lifetime. It seems that every time a question comes up about CBM, some try to explain it away by alluding to some vague rift or dispute that CBM supposedly had, and that seems to be what is happening here.
As for TEPaul's fanciful notion that NGLA never hosted an Amateur during CBM's lifetime because of of some supposed rift and/or parting between CBM and and USGA, caused by the election of R.H. Robertson as USGA president in 1901, it is unfounded to say the least. CBM was very much an important part of the USGA long after Robertson's brief (1901-1902) term as president of the organization. He continued to serve the USGA for a long time thereafter, including service on the Executive Committee and the Nominating Committee (which allowed him great control over who served the USGA.) He also headed various Rules committees and sat on the R&A's Rules Committee as a quasi-representative of the USGA interests, helped redraft the rules for both organizations, and he authored numerous changes to both the rules of golf and the USGA bylaws. In short, he continued to shape the future of the USGA and golf in America long after Roberson's tenure had come and gone.
It is true that CBM had serious issues with Robertson's ideas, particularly his lax treatment of the Amateur issue and his attempts to Americanize the game, but so did many of the other traditionalists at the USGA, and most of Roberson's ideas were defeated at Committee.
The notion that (prior to his book) CBM had never publicly expressed his disagreement with Robertson's proposed policies is simply not accurate. CBM and other traditionalists within the USGA had long been vocal public opponents of any policy (USGA or otherwise) with which they disagreed, and they were particularly vocal regarding the Amateur question and the controversial issue of Americanizing the game. Every time the Amateur question came up, CBM (and others) reminded the USGA that Robertson's lax approach was a mistake.
And as for CBM's feelings toward the leadership of the USGA and his supposed rift with the organization, I've never seen anything (other than petty gossip, of course) which leads me to believe there is too much to it. Surely there were rough spots along they way --as I said CBM was quite vocal when he felt like the soul of golf was at stake, but CBM was one of those running the organization, and he was close friends with many of those who were also serving. He speaks highly of many of them, and somewhere around one-half of the early USGA presidents were also members of NGLA!
Here is what CBM had to say about the leadership of the USGA in his 1928 book, at the close of his two chapters on the early history of the organization:
"Although the Western Golf Association repeatedly pounded on the doors of the U.S.G.A. Committee to change their rules in golf, and their constitution, thanks to the able leadership in the U.S.G.A. through their presidents, golf to-day is played practically the same way as it is in Scotland."