Segments creation is dropping stops. Speeds missing segments

[JabunchWork]

Two issues I am having are shown in the attached powerpoint.
1st: When segments are created, it seems that stops are being dropped on some routes.
an example is from Harrisonburg Va's GTFS.
The pink line stop times file shows for all trips
Stop sequence Stop
9 88895
10 88751
11 88771
But the segment created goes for stop sequence 9 goes from 88895 - 88771.
A similar example is for the green line.

Also: for trips going from 88871 to 88753 a segment is properly created, and the frequencies by segment correctly calculates the frequency. However, the segment doesn't exist in the speeds by segment output.

Do you have any thoughts on what is going on and how to fix these issues?

JAB
pythonfortransitissues.pptx
Passeo_GTFS_wstoptimes.zip

[JabunchWork]

So upon further investigation it seems that the dropping stops is related to routes that divert off a main road and loop down a local road to a neighborhood (one or more stops) then circle back along the same road to the diversion point and continue on the main road. While there are different shape points in the shape file for each direction, they are either on top of one another or very very close to the same path. Is this solveable?