John,
I use exactly the same setup as you (D300 / 10.5 / Nodal Ninja 5L). I think the problem that you are seeing could be caused by the camera sensor being off center. This would mean it would look like everything is centered but things would still be off. These are the setting that I use. Lower rail 59.5mm (well somewhere between 59mm and 60mm). Upper rail 81mm. When I shoot I also use a -15 degree tilt. If you upgrade to the full Nodal Ninja 5 then this angle will have a stop to lock at that position too.
A HDR example of this setup in action is here
http://www.bilsland.co.uk/greatwitleychurch/
I hope this sorts things out for you. If anything isn't clear enough let us know.
Bob Bilsland.