NOT resolved. Still happening to me in 2017.3.0f3. Unless I put a delay in, setting a transform position on an Instantiate-d game object does not work.

Same behaviour using 2017.3.0f3 and trying to add buttons to a canvas using:
GameObject button = Instantiate (buttonPrefab, canvas.transform.position + buttonOffset, Quaternion.identity, canvas.transform);

However doing the same thing over two lines works:
GameObject button = Instantiate (buttonPrefab, canvas.transform);
button.transform.position = canvas.transform.position + buttonOffset;

NOT fixed. Still happening in 2017.3.0f3

@manutoo - Definitely, that's what I was intending to do. However I spoke too soon - this is also broken over the network, so NetworkServer.Spawn(...) won't spawn remotely registered prefabs in the fixed server-location, but in the broken local client prefab location. Rather than refactor all of my instantiation code, I'll wait for Unity's fix. Apparently it may be in an update tomorrow (5.6.5) according to a developer on the forums.

@shadiradio,
possibly, you can backup all your prefab values at game start (or on 1st instantiation), and then restore the values on game exit (or simpler, only reset all prefab positions & rotations to 0 on game exit), so version control won't get too ugly... :)

@manutoo - Thanks again, it does work. It's pretty ugly with version control (as every single prefab is touched/modified), especially since I use a prefab object pooler for a lot of FX. But at least it's playable again.

@manutoo - Much appreciated! I wasn't aware that you can modify the prefab transform information before instantiating and they would be passed through. I'll give it a shot today - thanks.

@shadiradioI,
there's an easy workaround ; change from :
GameObject Obj = GameObject.Instantiate(m_FxPrefab, Pos, Rot) as GameObject;
to :
m_FxPrefab.transform.position = Pos;
m_FxPrefab.transform.rotation = Rot;
GameObject Obj = GameObject.Instantiate(m_FxPrefab) as GameObject;

If for some reason, you need the original prefab position & rotation somewhere else, then backup them & either use the saved values or restore them after the call to Instantiate().

Have this problem in 2017.2.0f3

Unfortunately, it's not in the patch notes for 5.6.4p4. I'm not sure how many weeks (months?) I'll have to delay my upcoming patch. Unity - if you think I'm being annoying, try making a game without knowing object positions.