I figured out what is going on. If one pastes in just those cells with filled in "big" numbers, then some of the pencil marks are different, since they are determined with just the information known for that grid.
What is being pasted in with the string I sent, has pencil marks that have been influenced by other parts of the samurai grid.
So, SudoCue is not using the pencil marks based on Samurai eliminations when it issues the initial "warning" message. However, it does use the pencil marks in the solver log, as evidenced by the fact that a solution is reached. The 6 that I thought was missing from the steps was in fact there, I just missed it.
The puzzle, with pencil marks based on the filled in cells truly does have more than one solution, but based on the additional pencil mark eliminations, does allow a unique solution to be determined. Bottom line, Ruud's message wording is just a little misleading. Oh well.
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