Hi, the segments which cannot converted to instances are placed in the RC pivot point, because are part of the non-instanced mesh.
In previous versions, this issue was not noticeable because these meshes were are attached in an unique object.
But with the new "Separated Meshes" option, it's possible to generate individual objects (although with the pivot placed in that way).
I will take a look if it's possible to move the pivot point to the segment, which should be more correct.
Anyway, there is a simpler way to align the pivot: just turn off Deform->Bend and Slice in the Segment properties (within the style).
Doing that, segments can be generated as instances, and generated by RailClone Tools with their pivot aligned locally.