To reproduce this bug:

1. Open the attached project
2. Open 'test' scene
3. Example on top: connected in the editor before runtime
- right: two connected objects without rotation
- left: two connected objects WITH rotation (both the same angle, relative to each other it's the same construction)
The objects are disconnected and connected again in the 'control' script in Start(), it doesn't change anything about their behaviour.
4. Example on bottom: NOT connected in the editor before runtime
-right: two connected objects without rotation
-left: two connected objects WITH rotation (both the same angle, relative to each other it's the same construction)
- The objects are connected in the "control" script in Start()
5. Play the scene
6. Notice the bottom left behaviour looks different
7. It seems to be a problem with calculating the reference angle

Captured repro: http://screencast.com/t/Oew4kyGJe2JV