Able to repro in Chrome 53. The footer randomly updates its vertical position as the viewport is resized.
In Chrome 54 it's better but not perfect. The footer updates its vertical position when the width changes but not when the height changes.

This doesn't actually need any flexbox -- the attached testcase has the issue, too (showing up slightly differently -- when resizing smaller, the footer stays outside of the viewport)

Deleted: x.html 506 bytes

x.html 506 bytes View Download

Able to reproduce on Windows 10, Ubuntu 14.04 and Mac OS 10.11.6 using chrome stable #53.0.2785.116 and the reported chrome version #52.0.2743.116.

Bisect Information:
=====================
Good build: 45.0.2430.0
Bad Build : 45.0.2433.0

Change Log URL: https://chromium.googlesource.com/chromium/src/+log/76af67653a03212a3d9104e3a94a44d773917214..7ec6a579b7e47f84b384b98b6f04ee65beb55758

From the above change log suspecting below change
Review URL: 
https://codereview.chromium.org/1174343003

yukishiino@ - Could you please check whether this is caused with respect to your change, if not please help us in assigning it to the right owner.

I'm quite sure that my CL mentioned has nothing to do with the issue.  I guess that the issue was caused by Blink.

krajshree@, may I ask you to do a more detailed bisect?

https://chromium.googlesource.com/chromium/src/+log/76af67653a03212a3d9104e3a94a44d773917214..7ec6a579b7e47f84b384b98b6f04ee65beb55758
where we can see "Roll src/third_party/WebKit 65258a2:55df775 (svn 197117:197124)" for example.  Can you bisect which roll of WebKit caused the issue?  Then, I think you can find a better owner.

Able to reproduce the issue on Windows 10, Ubuntu 14.04, Mac OS 10.11.6 using chrome stable #53.0.2785.116, reported chrome version #52.0.2743.116 and latest canary #55.0.2872.0.

Bisect Information:
=====================
Good build: 45.0.2432.0	
Bad Build : 45.0.2433.0

Change Log URL: https://chromium.googlesource.com/chromium/src/+log/d9418440b42c22114448813f8d8341d22c9c0a51..fcbc256d04f63d5ef61b481e3a984a2c65e238ce

Blink changelog:
https://chromium.googlesource.com/chromium/blink/+log/97081fe..ddd1e8f

From the above change log suspecting below change

Review URL: https://codereview.chromium.org/1172153004

skobes@ - Could you please check whether this is caused with respect to your change, if not please help us in assigning it to the right owner.

Steve, could you take a look at this when you get a chance? Looks like it was caused by your change https://codereview.chromium.org/1172153004

Patch up: https://codereview.chromium.org/2429113002/

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/1abcf254f3e55be39879ca76d268192faf64a254

commit 1abcf254f3e55be39879ca76d268192faf64a254
Author: skobes <skobes@chromium.org>
Date: Thu Oct 20 17:17:17 2016

Don't update height in LayoutBlock::markFixedPositionObjectForLayoutIfNeeded.

This prevented LayoutBlockFlow::layoutBlockFlow from seeing that the height had
changed.  As a result, it failed to set relayoutChildren = true.

The bug affects fixed-pos objects in abs-pos containers, so it got worse with
http://crrev.com/1172153004 but existed before.

An equivalent patch for width was made in http://crrev.com/171463003.

Additionally, update the early return for the case where the abs-pos container
is the LayoutView.  (This is just an optimization.)

BUG= 640639 

Review-Url: https://chromiumcodereview.appspot.com/2429113002
Cr-Commit-Position: refs/heads/master@{#426515}

[add] https://crrev.com/1abcf254f3e55be39879ca76d268192faf64a254/third_party/WebKit/LayoutTests/fast/block/positioning/fixed-in-abs-height-change.html
[modify] https://crrev.com/1abcf254f3e55be39879ca76d268192faf64a254/third_party/WebKit/Source/core/layout/LayoutBlock.cpp
[modify] https://crrev.com/1abcf254f3e55be39879ca76d268192faf64a254/third_party/WebKit/Source/core/layout/LayoutBox.cpp
[modify] https://crrev.com/1abcf254f3e55be39879ca76d268192faf64a254/third_party/WebKit/Source/core/layout/LayoutBox.h

Verified in canary (56.0.2897.0).