This is the intended behavior of ScrollAnchoring: https://github.com/WICG/ScrollAnchoring/blob/master/explainer.md
You can disable it on the container element via CSS:

.board {
  overflow-anchor: none;
}

that helps, however without it we're getting wrong value for the event.pageY (see "chrome2 scroll pageY.htm")

seems that adding 'overflow-anchor: none;' on the fly doesn't help immediately, it's almost like it needs to pass some time for the cache to clear or something. So you have to have it in css on page load, doing $board.css('overflow-anchor', 'none') before the append or even on mousedown won't help; even if you set it with the chrome tools it doesn't help immediately.

Able to reproduce this issue on reported version 62.0.3202.94 and on latest canary 64.0.3277.0 using Mac 10.12.6 , Windows 10 and Ubuntu 14.04 with attached HTML files in comment#0.

Bisect Info:
===============
Good Build: 56.0.2895.0
Bad Build: 56.0.2896.0

You are probably looking for a change made after 418714 (known good), but no later than 418715 (first known bad).
  https://chromium.googlesource.com/chromium/src/+log/02a4849687aa7a52e3af8959484f7f8b6b9335cf..73693c4b2eb516e55b700c0317b38d672a0bdb29

Review-Url: https://codereview.chromium.org/2335363003

Suspecting same from changelog.

@skobes: Please confirm the issue and help in re-assigning if this is not related to your change.

Thanks!

The value of MouseEvent.pageY is determined before the event handlers are invoked.  If an event handler modifies the scroll position (even indirectly via scroll anchoring), the pageY value isn't automatically adjusted for subsequent handlers of the same event.  I think this explains the behavior you're seeing in "chrome2 scroll pageY.htm".

Failure of applying "overflow-anchor: none" to .board on the fly looks like a bug (though not a P1 regression).

A different workaround is to explicitly restore the scroll position after rearranging the DOM, e.g.:

  var saved_scrollTop = document.scrollingElement.scrollTop;
  hovered.before(plh);
  document.scrollingElement.scrollTop = saved_scrollTop;

that's pretty much the workaround that I'm using right now, 
if the container doesn't have 'overflow-anchor': none; and the $(window).scrollTop() is different than the saved one I set it back $(window).scrollTop(savedScrolTop)

As this seems to work as indented I closed it for now.