Able to reproduce the issue on windows 10 and Ubuntu 14.04 using chrome/61.0.3163.79 
Note: we will update the mac behaviour soon

Manual Bisect Info: 
=============== 
Good Build: 60.0.3112.0(474897)
Bad Build:   61.0.3113.0(475195)

After performing the per revision bisect, tool provided irrelevant CL might not be the root cause for this issue. Will check this again and provide the right bisect information soon.

CL: 
  https://chromium.googlesource.com/chromium/src/+log/ce390470c7c40222140f1897f7405bc475d2f1a7..2f1f15df30c885442a19667207c8b488602572

Tested the issue with steps mentioned below, able to reproduce the issue on the reported version 61.0.3163.79 stable and on latest canary 63.0.3216.0 on Ubuntu 14.04 and windows 10 with the below mentioned steps.
1. visited a bunch of websites over time.
2. enabled cookies and third party cookies
3. tapped Ctrl+Shift+Delete to bring up the ""Clear browsing data"" window. 
4. Selected ""Clear the following items from the beginning of time."" 
5. Enabled (checkmark) all removal options (so everything is being cleared). 
6. Clicked the blue ""CLEAR BROWSING DATA"" button (or press Enter).

The issue is showing inconsistent behavior by clearing cookies at one point of time and if rechecked on the same build the cookies aren't getting cleared. This issue is also seen on M50-50.0.2624.0 .  Hence, marking the issue as untriaged for further updates.

zapahjpzn: could you check chrome://settings/content/cookies to see what data is left after deleting cookies?
It sometimes takes a moment until all data is removed. 
Please reload the page after 30s and check again. If you still have entries, please upload a screenshot about the data that is left after clearing cookies.

 Issue 773743  has been merged into this issue.

This is probably related to  https://crbug.com/769425  and should be solved in Chrome 63. 
The data is deleted but some empty entries remain until restart. Could you try Chrome Canary and see if you still have this issue? If the issue remains, please reopen.

@dullweber

I can confirm that after "clearing browsing data," relaunching Chrome does indeed remove the entries from the Cookies list; however, just so it is clear to you guys, ALL Chrome processes must be relaunched.

Say there are 3 profiles each with a browser window open and there are 3 apps running (again each with its own window). All 3 profile windows and all 3 app windows must be relaunched for the "deletion" to be shown. If any one of those 6 windows is not relaunched, then cookies/browsing-data in ALL profiles will remain (ie, be visible as if not deleted).

Thanks for your response! The issue is solved in Chrome 63. The beta should be available very soon if you would like to try it out.

If you have multiple Windows, you can quickly close all of them using "Exit" from the menu. All Windows and Profiles will be restored on next start.

Will Chrome 63 still require closing all windows to effectuate the "cleaning"? Do the developers consider this "an issue"? They should.

Another gripe I have with closing multiple windows (as described) is that there is no separation between profiles. If I clear all browser content for user "John", 1) I should not have to close the window to make this effective and 2) I should not have to close user "Mary" browser window to "effectuate" John's browser clearing command. Chrome is multi-process. The profiles should be separate and distinct in process and not be tied like they are, requiring multiple profiles to be closed before one profile's data can be cleaned.

Also, what about users who have configured Chrome to NOT remember browser data when the window is closed? It seems Chrome does not respect that configuration if the window is just restored after Exit. And if a PROFILE configures the data to be cleared on close but this only happens when ALL profiles are closed, that Profile owner is misled by the settings because his/her data are not being cleared when his browser window is closed (it only gets cleared when ALL browser windows (ie all profiles) are closed). This should be fixed.

Not having History appear everywhere in the browser is not just about privacy, it is also an ease-of-use issue. Having the URL-bar and dropdown etc fill with history negatively affects user searches and gets in the way of using the browser effectively--if I type something in the omnibar and press enter, I want what I typed to be searched for. But constantly, Chrome adds to what I typed and searches for something entirely different. This drives me NUTS. (Often I'm typing/copying something from an un-highlightable section of a webpage and am not seeing what's happening in the omnibar as I type).

Also, having History items fill up the omnibar-dropdown crowds space and pushes out Bookmarks (which is really what I want to see). There should be a way to completely disable History for ease-of-use reasons.

Chrome's over-use of History (and failing to clear data when requested along with restoring windows after exit is one of the things I constantly have to fight against when using Chrome). When I clear "Everything," every thing should be cleared right then and there. I should not have to close the window to see the result.

Chrome's over-use of History results in "crud" making omnibar use a PITA which necessitates constant "cleaning" to keep the omnibar usable. It's Chrome's achilles heel and it's completely fixable.

Having to close a window to get rid of these empty entries is a bug and is fixed in Chrome 63. It was caused by localstorage not removing empty entries until Chrome is fully closed. The actual data was deleted correctly.

If some data still can't be removed correctly please file a bug, this is considered an issue. You can CC me in this case as I'm currently looking into these issues.

If you don't want Chrome to remember any cookies or history, how about using Incognito mode?

You can configure whether Chrome restores your session in settings. (section "On startup")

If you select to not keep cookies when you quit Chrome and this doesn't work correctly, please also file a bug.