Interestingly enough, probably one of the few (if only?) times where the movie is an improvement over the book. Not that Mr. Condon's novel was lacking, per se, it just doesn't pack the emotional wallop that Frankenheimer's film did. His visual approach explodes off the screen whereas the novel is very journalistic and matter of fact.

Has anyone ever found an explanation for the really weird dialogue on the train between Sinatra and Janet Leigh?

You can view the script here. The scene I'm referring to begins with the slug:

EXT. TRAIN - DELAWARE, EN ROUTE TO NEW YORK - DAY