Open in new window option

Judi,Not quite. If you are referring to the option on publish:"The published course will be presented in a separate window from the LMS"then the real meaning of that option is to tell the published content that the LMS will not close the window that the content is running in after the LMSFinish is issued (the LMS should, but that's another discussion). All bookmarking and everything else will work the same regardless of this option.However, if you are talking about within a course you have an action to go to another page in the content and you select the option on the action to open that page in a new window, then yes, bookmarking for the newly opened window will not effect bookmarking ... only the main window/frame launched by the LMS will do bookmarking.Tim