Steps to reproduce this issue:

- Open the attached project
- Open 'bug' scene
- The two green spheres visualize the ends of the collider
- Play the scene with gizmos on
- Observe Scene with Right orthographic view to see 3 expected collisions (the sweep direction is -x).

Observe:

1. Hit on blue sphere is correct
2. Hit on brown sphere is completely wrong position
3. Pink sphere is incorrectly missed

The problem seems to happened whenever the radius is not 1

Worked fine in 4.6