To reproduce:
1. Open attached project;
2. Open "scene.unity";
3. Enter Play mode;
4. Instantiate a new UI block by pressing "S";
5. Press "F" to take the block and apply localScale 1,1,1 & localPosition 0,0,0;
6. Repeat 4th step and notice the difference;
7. Change Canvas Render Mode to Camera by pressing "A";
8. Instantiate a new UI block by pressing "S";
9. Notice that UI block has localScale 935.307 and localPosition.Z = 8417.768.

Expected result: newly instantiated UI elements should inherit their prefab localScale and localPosition.
Actual result: when Canvas Render Mode is set to Overlay, newly instantiated UI elements get localScale = 1.510622, when Canvas Render Mode is set to Camera, newly instantiated UI elements get localScale = 935.307 and localPosition.Z = 8417.768 despite the fact, that prefab has localScale = 1 and localPosition (0,0,0).

Reproduced on versions: 5.5.4p2, 5.6.3f1, 2017.1.0p3, 2017.2.0b6, 2017.3.0a2.