The velocity reporting for steppers in NI-Motion 6.1.2 can be slightly incorrect at low step speeds with 733x and 734x boards because of a fixed point calculation error - this is ONLY a reporting error and the steppers WILL move at the correct speed. This has been fixed with NI-Motion 7.0.
The Primary and Secondary feedback channels can no longer be set in MAX starting with NI-Motion 7.0, however, they can be set through the Motion API in LabVIEW, CVI, etc. This change was made to reduce the complexity of the interface in MAX.
Hopefully this explains better the behavior of what you were seeing.