Back to Chrome and PDF Viewer, it is a recent change that Chrome implements its own PDF Viewer for security reasons and will not allow many of the old extensions it used to for PDF Viewing inside of the browser itself.
All current documentation indicates that you must go the "about:plugins" route, etc., that I documented a while back to get Chrome to trigger your system PDF viewer of choice. The various checkboxes within Adobe Reader or similar will have no effect on or interaction with Chrome.
