1. On the D200 Custom Setting a6 is the correct menu item to set the camera to use the AF-On button only (or to set using both). Custom Setting a5 is the "Lock On" setting which deals with how the autofocus system reacts when something temporarily comes between the camera and a previously focused subject - it has nothing to do with the use of the AF-On button.
2. As far as I know, with a "D" lens you cannot manually focus unless you first disconnect the lens from the camera's AF system by changing the AF selector switch to "M." (There might be some D lenses that have an AF-Manual switch, but I've never seen one.) An AF or AF-D lens uses a mechanical connection to a motor in the camera body to operate the lens focus (often referred to as a "screwdriver drive"). An AF-S lens uses a motor in the lens itself to move the focus mechanism based on electrical signals from the camera. With an AF or AF-D lens you must disconnect the mechanical focus drive from the body so that you can manually focus. If you force the lens focus ring with the mechanical AF drive connected you can damage the lens, the camera, or both. With an AF-S lens it can be set to allow both AF or Manual operation. In this case, the lens recognizes when you turn the focus ring manually and ignores the electrical signals from the camera's AF system (at least until you release and then press again the AF-On button, or the shutter release if the camera is set to focus with the shutter release). So your question "Could it be the lens/body combination" is correct. As far as I know only AF-S lenses can be manually focused while the AF system is still engaged. ...or manual focus lenses, of course.