Henduck,
I have the Marantz DV-8400, and have been playing SACD and DVD-A discs perfectly in 5.1 and Stereo every since I purchased the unit last June. DVD Video looks great, as well. I've been extremely happy with the unit, and would think that the 6400 would have reasonable performance, as well. The 8400 automatically displays whether or not the disc has true 5.1 surround information, or just 2 channel information, and handles it accordingly. Perhaps you should check your manual again to ensure your setup options were properly configured.
Good Luck,
Pat