Launch_Story.exe not bookmarking when story.html does

We created a custom skin for our player that has a built in exit button that closes the window with, presumably, the same functionality as the browser close button.

Both the in-course Exit button and the browser close button bookmark properly when the course is opened via story.html.

If Launch_Story.exe is used to open the course, the window close button bookmarks properly, but the in-course button closes the window without bookmarking.

What could be causing this functionality mismatch?