Reproduction steps:
1. Download and duplicate attached Unity project.
2. Open first project with 5.1 version of Unity and add "milk_pr", "fish_pr" and "cocktail_pr" assets to the scene.
3. Repeat step 2 for second-duplicated project with 5.2+ version of Unity.
4. Compare relative coordinates of both projects for those game objects(GIF attached).

Actual result: children objects coordinates differs between 5.1 and 5.2+ version of Unity.
Expected result: same coordinates with 5.1 and 5.2+ versions of Unity.

Reproduced with: 5.2.0p1, 5.2.3p2, 5.3.0f3
Not reproduced with: 5.1.4p1