Nick,
The issue is with the clamp mounted on the lower rotator. In the stock configuration, the knob is too long and overlaps the tripod leg in the Nadir patch shot.
Replacing the long knob with a shorter one that comes on a different clamp helps, but not enough. A low profile knob will fix this issue. Since it is almost impossible to accuratly move the tripod over the exact same distance each and every time, the more open space there is between components in the Nadir and the Nadir patch, the easier it is to apply the patch shot.
Old dogs do not want to learn new tricks. I don't want to take one little extra Nadir picture rotated 180 degrees apart from the first one, dag nab it!
Dennis