Steps to reproduce:
1. Open attached project's scene "Scale Bug".
2. Enter play mode.
3. Cube starts to scale even though it is only rotated by the script:

"Obj.SetParent (Scaler, true);
Obj.rotation = Quaternion.AngleAxis Time.realtimeSinceStartup, Vector3.up);
Obj.SetParent (null, true);"

Notes: disabling worldPositionStays (Obj.SetParent (null, false)) - does not scale cube anymore.
Using transform.parent = Scaler works the same as Obj.SetParent(Scaler, true).

Reproduced on 5.4.0b9, 5.3.3p1 and 5.1.0f3.