System Information
Windows 8.1
Intel HD 4600
NVIDIA GeForce GTX 960M

Blender Version
Broken: (example: 2.75a Hash c27589e, see splash screen)
Worked: (optional)

Short description of error
Custom Orientation Axis created with an Edge is not align with the parent Edge.

Exact steps for others to reproduce the error

Do an scale on the Z axis on the initial Cube : S Z 0.5
Goto Edit Mode
Translate the vertical edge in the positive X and Y quadrant : G Y -1
Make a Scale of the face in parallel to Y axis (X positive) : S Z 0.2
Create an custom Transform Orientation with any edge parallel to the X axis.

Based on a (as simple as possible) attached .blend file with minimum amount of steps