Able to reproduce the issue on Ubuntu 14.04, Windows 7 and Mac 10.12.6 with the reported version 62.0.3202.0 dev and latest canary 63.0.3208.0.

Manual Bisect Info
===============
Good Build: 57.0.2929.0
Bad Build: 57.0.2931.0

You are probably looking for a change made after 434145 (known good), but no later than 434146 (first known bad).

CHANGELOG URL:
https://chromium.googlesource.com/chromium/src/+log/033fbea1cde6401bacabe4b721f21ba41215ee23..0bbe3ad45b8fec1cfa264b69db7eb6900852a9b7

From the above change log suspecting the same.

@dullweber: 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.

This is currently working as intended. We changed content settings to not be inherited in incognito unless they are less permissive than the default.

The CL description states that popups are not affected but after some discussions, we decided to also apply this behavior to popups for consistency and there was no negative feedback yet.

Why would you like to have popups enabled in incognito?

 Issue 732422  has been merged into this issue.

I actually found one other case

I always use incognito mode when making payment or financial transaction.

In my country, there are some local websites require popup blockers to be disabled, when making payment. Some local websites, when I try to make payment, the payment websites open my bank's online banking site in a popup window.

Some local websites use third party payment service provider. When I make payment, these websites redirect me to payment service provider's website which I don't even know the URL. Therefore, not possible to whitelist the payment website.

I will always use incognito mode for online payment. Therefore, please allow me to disable popup blocker in incognito mode.

I understand. You should still be able to use your banking site by clicking on the "popup blocked" notification and then on the url that was blocked.

Do you know what is session? Sometimes, when making payment, we are told not to refresh the page nor clicking the back button, or else an error will be displayed. If popups were blocked, and we try to allow the popups, we need to refresh the page again to make the popups working. Abd, once we refresh, an error occur, and we need to restart doing everything again. E.g. if we are booking flight, we may need to restart the booking process, reselect flight, reenter passengers information, etc, and the air ticket price may be increased. The solution to this is to turn off popup blockers.

Seriously, what is the point of not allowing incognito mode to inherit content settings from normal mode? I don't see any benefits at all.

Until this issue has been fixed, I will stop using Google Chrome for private browsing.

If you really don't want incognito mode to inherit content settings, I have a suggestion. You can create separate content settings for incognito mode.

Right, some websites implement sessions in really weird ways that break browser navigation.
I will think about whether we should revert the incognito inheritance behavior for popups. 

As a workaround I would suggest to create a second chrome profile (click on your name in the top right -> manage people -> add person) and then for this profile go to chrome://settings/content/cookies and enable "Keep local data only until you quit your browser". This way you should get signed out when you close the last window of this profile, similar to incognito but your content settings will be kept. Would that work for you?

No. Your suggestion, while I am not sure about cookies, I still need to manually clear the cache and history before I exit Chrome. I use incognito mode because I want no cache, no history, no cookies, etc, totally nothing was kept.

I am now using Firefox which still allow popups in private browsing. I am not going to use Google Chrome until you bring back the feature.

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/bec18d37c70ed7671f734feacaffb070aac2c650

commit bec18d37c70ed7671f734feacaffb070aac2c650
Author: Christian Dullweber <dullweber@chromium.org>
Date: Mon Nov 13 11:06:00 2017

Inherit popup permission to incognito mode

This changes the popup permission to be inherited to incognito profiles.
While other content settings are not inherited due to security or privacy
concerns, inheriting sites allowed to show popups is save.

Bug:  762349 
Change-Id: Ia31f6cea46edf8c705302ee4a414a40a8321756e
Reviewed-on: https://chromium-review.googlesource.com/672547
Reviewed-by: Raymes Khoury <raymes@chromium.org>
Commit-Queue: Christian Dullweber <dullweber@chromium.org>
Cr-Commit-Position: refs/heads/master@{#515921}
[modify] https://crrev.com/bec18d37c70ed7671f734feacaffb070aac2c650/chrome/browser/content_settings/host_content_settings_map_unittest.cc
[modify] https://crrev.com/bec18d37c70ed7671f734feacaffb070aac2c650/components/content_settings/core/browser/content_settings_info.h
[modify] https://crrev.com/bec18d37c70ed7671f734feacaffb070aac2c650/components/content_settings/core/browser/content_settings_registry.cc
[modify] https://crrev.com/bec18d37c70ed7671f734feacaffb070aac2c650/components/content_settings/core/browser/content_settings_registry_unittest.cc

Popups and other non privacy sensitive permissions are inherited to incognito mode again.