This is happening throughout my company and on multiple types of printers; I'm 98% certain it's not a print driver issue.
When we print a document containing comments/tracked changes (displaying "balloons"), the landscape sections are printing as portrait if we print the entire document. Print Preview displays it correctly; printing only the landscape section prints it correctly; or printing "document only" (not displaying the balloons) prints it correctly. Unfortunately (as you've already guessed) the people I support aren't willing to accept any of those solutions.
Does anyone know if there's a fix for this? Does MS have a patch?