After some investigation,

Minimized repro: https://jsbin.com/yabepiz

It has something to do with the padding-top changing on body when the nav bar is hidden. Still need to investigate as to why this is happening. 

After more investigation, this seems like one of the fundamental problems of scroll anchoring.

It can be reproduced without the nav bar and has to do with js reacting to the adjustment that we make.

Minimized repro: https://jsbin.com/fenugo

The minimized repro above calls a function every 20 ms that changes the padding-top of the body element from 100px to 50px if the scroll position is > 300 (and vice-versa if scroll position < 300).  

So this is what happens:
1. The user scrolls just past the 300px point
2. The js on the page changes the padding-top on the body from 100px to 50px.
3. ScrollAnchor sees this change, and adjusts the scroll offset by 50px upwards.
4. The js on the page sees that the scroll offset < 300px and changes the padding back to 100px.
5. ScrollAnchor sees this change, and adjusts the scroll offset by 50px downards.
6. The js on the page sees that the scroll offset > 300px and changes the padding to 50px
7. repeat from step 3

I guess the problem in general is that if the site itself is making adjustments, then our adjustments may cause undefined behavior.

 Issue 603246  has been merged into this issue.

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/2fd28b5102e73c49b3891d9bc7c05ffda979e2ea

commit 2fd28b5102e73c49b3891d9bc7c05ffda979e2ea
Author: skobes <skobes@chromium.org>
Date: Wed May 18 21:27:18 2016

Implement bounce suppression in ScrollAnchor.

An element can "bounce", by making the inverse of its last movement, when a
scroll anchoring adjustment interacts with a scroll event handler that changes
layout at a scroll offset threshold.

ScrollAnchor now detects bounces by tracking the most recent adjustment and the
element that triggered it (even if we have anchored to a different element since
then), and suppresses repeat bounces.

BUG= 598233 , 601906 , 603376 

Review-Url: https://codereview.chromium.org/1971423002
Cr-Commit-Position: refs/heads/master@{#394552}

[add] https://crrev.com/2fd28b5102e73c49b3891d9bc7c05ffda979e2ea/third_party/WebKit/LayoutTests/fast/layout/scroll-anchoring/onscroll-bouncing.html
[modify] https://crrev.com/2fd28b5102e73c49b3891d9bc7c05ffda979e2ea/third_party/WebKit/Source/core/layout/LayoutObject.cpp
[modify] https://crrev.com/2fd28b5102e73c49b3891d9bc7c05ffda979e2ea/third_party/WebKit/Source/core/layout/ScrollAnchor.cpp
[modify] https://crrev.com/2fd28b5102e73c49b3891d9bc7c05ffda979e2ea/third_party/WebKit/Source/core/layout/ScrollAnchor.h

@skobes, the top nav judder issue still exists on TC with the debouncing fix above. I didn't get a chance to dig into it further.

Exciting - the original Techcrunch page has:

@media (max-width: 29.74em) body {
  transition: padding-top .2s ease-in-out;
}

The intermediate states of the animation defeat the bounce suppression. :(

Lol. We should go back to the drawing board on how to address this then. :)

I don't actually see this on that techcrunch page. I see a brief flicker, but the bounce suppression seems to be working.

This still repros for me with mobile emulation.

I wish we had a more generic solution to the JS cycle problem ( issue 604996  has more discussion of it).  Right now the best option I know of is to set a fixed limit (say 50) on the number of adjustments made between user scrolls.

FYI, here is what it looks like with a limit of 20 adjustments between user scrolls.

Deleted: bounce-with-limiter.mp4 735 KB

	bounce-with-limiter.mp4 735 KB View Download

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/34ae0389f0c660c23f691595341188acc5444e00

commit 34ae0389f0c660c23f691595341188acc5444e00
Author: skobes <skobes@chromium.org>
Date: Fri Jul 01 18:48:25 2016

Limit ScrollAnchor to 20 adjustments between user scrolls.

This somewhat mitigates the impact of pathological feedback loops with scroll
event handlers.

BUG= 601906 

Review-Url: https://codereview.chromium.org/2118683002
Cr-Commit-Position: refs/heads/master@{#403491}

[add] https://crrev.com/34ae0389f0c660c23f691595341188acc5444e00/third_party/WebKit/LayoutTests/fast/layout/scroll-anchoring/feedback-loop.html
[modify] https://crrev.com/34ae0389f0c660c23f691595341188acc5444e00/third_party/WebKit/Source/core/layout/ScrollAnchor.cpp
[modify] https://crrev.com/34ae0389f0c660c23f691595341188acc5444e00/third_party/WebKit/Source/core/layout/ScrollAnchor.h

This still looks janky but no longer gets stuck forever.  I don't know anything else that can be done here, so closing.