Unity 5.5 to 2017 -> Broken Animation Layers?

Today I transferred my big project to unity 2017 from unity 5.5 and there is some errors I can fix, but there is something wrong with animation layers I don't know how to fix yet.

I was using two synced legs layers to animating player's upper body animations to look more realistic (one layer with mask which take just legs with ik, and other which only animates root)
Now when this layers are in use, players legs don't even bend and it looks totally wrong
What was changed in this mechanics in Unity 2017?

Other thing is that some animations with root motion are translating character position totally wrong, precisily, animations from free mocap (on unity 5.5 everything was right), animations from bought mocap are translating correctly.

Edit:
In 2017 when I remove root from layer mask legs stops bending in animation!!!

 

Hi Nirvan

this is not something we are aware of, please log a bug and we will investigate

 

Unfortunately today I'll not have enough time, but I just noticed something interesting.
I think all is because "Foot IK" in animation state option which behave different than before.
This option mostly settings legs of my character in the way I want.
But in unity 2017 it seems like when player is running Iks trying to reach some points under ground to plant foots instead of grounding.
Here I attach screenshot of what is going on.

Is there a way to have access to set some parameters of this IK?

 

Somehow I finally reproduced both issues.
I made small projects and reported with Bug Reporter.

I hope it will be fixed soon, last time when I sent raport about broken occlusion culling I was waiting 2 months for reply :/

We went to unity 2017 and wanted to make update for people (MMO game) in this week, but this issues not allowing us to do it. Please put this issues in resonable priority if it is possible.

I guess I'll describe in short what's going on:
Bug with Ik occurs only when we use "Foot IK" option in animation state in other animator layer which have weight > 0 (othervise ik and layer is disabled) and when other layer have blend tree with indirect value so animations are blending. When animations aren't blending ik works right.

Error with root motion is strange because it looks like only some animations have this problems, not all.
When I have animation with root motion and there are any layer with weight over 0 root motion translation is broken.

This both things was working right in Unity 5.5