I can repro in 55.0.2858.0 canary (64-bit) but not in 53.0.2785.101 m (64-bit) so this seems like a regression.

You are probably looking for a change made after 408064 (known good), but no later than 408071 (first known bad).
CHANGELOG URL:
  https://chromium.googlesource.com/chromium/src/+log/e8d5056..32dad58?pretty=fuller

looks like https://codereview.chromium.org/2075103002 -> lshang

This CL was initially in 54.0.2810.0 so it's actually in M54 already? Please address this as soon as possible since this seems like quite a serious regression to me.

Thanks for catching. lshang@ I think we should probably revert the cookies change on ToT and merge the fix to M54. 

We should investigate why this is happening though, as discussed.

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/88f013bd979ec30333bd7ce6c0bd2e0b5f6f2742

commit 88f013bd979ec30333bd7ce6c0bd2e0b5f6f2742
Author: lshang <lshang@chromium.org>
Date: Tue Sep 13 14:08:20 2016

Revert cookies back to be domain scoped

Revert cookie scoping back to domain-based.

BUG= 645745 

Review-Url: https://codereview.chromium.org/2337873002
Cr-Commit-Position: refs/heads/master@{#418233}

[modify] https://crrev.com/88f013bd979ec30333bd7ce6c0bd2e0b5f6f2742/chrome/browser/browsing_data/cookies_tree_model_unittest.cc
[modify] https://crrev.com/88f013bd979ec30333bd7ce6c0bd2e0b5f6f2742/chrome/browser/content_settings/host_content_settings_map_unittest.cc
[modify] https://crrev.com/88f013bd979ec30333bd7ce6c0bd2e0b5f6f2742/components/content_settings/core/browser/content_settings_registry.cc
[modify] https://crrev.com/88f013bd979ec30333bd7ce6c0bd2e0b5f6f2742/components/content_settings/core/browser/host_content_settings_map.cc
[modify] https://crrev.com/88f013bd979ec30333bd7ce6c0bd2e0b5f6f2742/components/content_settings/core/browser/website_settings_info.h

The revert has landed - let's see if it fixed OP's problem when it gets to Canary and merge it.

The migration to origin scoping has been reverted much earlier, so there's nothing more to do there. But we might want to consider doing backwards migration (on the same heuristic principle - assuming that all non-wildcard exceptions are wrong) to fix it retrospectively for users like the bug reporter.

More importantly, we could take advantage of these changes and of what we have learned from the problems with the migration, and finally get the cookie scoping right - and that's not to ContentSettingsPattern::FromUrl(), but to the eTLD+1.

Requesting merge of #8 to M54. We did some migration in M54 and this cookie bug occurred due to the migration. This revert fix has been verified on Canary. Merging it to M54 so that the bug won't go into stable.

Your change meets the bar and is auto-approved for M54 (branch: 2840)

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/8f5dd2a6fd71dbf05fcd87524d3a53aa3b9696c8

commit 8f5dd2a6fd71dbf05fcd87524d3a53aa3b9696c8
Author: Raymes Khoury <raymes@chromium.org>
Date: Thu Sep 15 02:43:04 2016

Revert cookies back to be domain scoped

Revert cookie scoping back to domain-based.

BUG= 645745 

Review-Url: https://codereview.chromium.org/2337873002
Cr-Commit-Position: refs/heads/master@{#418233}
(cherry picked from commit 88f013bd979ec30333bd7ce6c0bd2e0b5f6f2742)

Review URL: https://codereview.chromium.org/2342743002 .

Cr-Commit-Position: refs/branch-heads/2840@{#372}
Cr-Branched-From: 1ae106dbab4bddd85132d5b75c670794311f4c57-refs/heads/master@{#414607}

[modify] https://crrev.com/8f5dd2a6fd71dbf05fcd87524d3a53aa3b9696c8/chrome/browser/browsing_data/cookies_tree_model_unittest.cc
[modify] https://crrev.com/8f5dd2a6fd71dbf05fcd87524d3a53aa3b9696c8/chrome/browser/content_settings/host_content_settings_map_unittest.cc
[modify] https://crrev.com/8f5dd2a6fd71dbf05fcd87524d3a53aa3b9696c8/components/content_settings/core/browser/content_settings_registry.cc
[modify] https://crrev.com/8f5dd2a6fd71dbf05fcd87524d3a53aa3b9696c8/components/content_settings/core/browser/host_content_settings_map.cc
[modify] https://crrev.com/8f5dd2a6fd71dbf05fcd87524d3a53aa3b9696c8/components/content_settings/core/browser/website_settings_info.h

Please mark security bugs as fixed as soon as the fix lands, and before requesting merges. This update is based on the merge- labels applied to this issue. Please reopen if this update was incorrect.

For more details visit https://www.chromium.org/issue-tracking/autotriage - Your friendly Sheriffbot

Note that this affected a very specific UI path - it was still possible to block cookies through several other UI entrypoints.

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The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/8f5dd2a6fd71dbf05fcd87524d3a53aa3b9696c8

commit 8f5dd2a6fd71dbf05fcd87524d3a53aa3b9696c8
Author: Raymes Khoury <raymes@chromium.org>
Date: Thu Sep 15 02:43:04 2016

Revert cookies back to be domain scoped

Revert cookie scoping back to domain-based.

BUG= 645745 

Review-Url: https://codereview.chromium.org/2337873002
Cr-Commit-Position: refs/heads/master@{#418233}
(cherry picked from commit 88f013bd979ec30333bd7ce6c0bd2e0b5f6f2742)

Review URL: https://codereview.chromium.org/2342743002 .

Cr-Commit-Position: refs/branch-heads/2840@{#372}
Cr-Branched-From: 1ae106dbab4bddd85132d5b75c670794311f4c57-refs/heads/master@{#414607}

[modify] https://crrev.com/8f5dd2a6fd71dbf05fcd87524d3a53aa3b9696c8/chrome/browser/browsing_data/cookies_tree_model_unittest.cc
[modify] https://crrev.com/8f5dd2a6fd71dbf05fcd87524d3a53aa3b9696c8/chrome/browser/content_settings/host_content_settings_map_unittest.cc
[modify] https://crrev.com/8f5dd2a6fd71dbf05fcd87524d3a53aa3b9696c8/components/content_settings/core/browser/content_settings_registry.cc
[modify] https://crrev.com/8f5dd2a6fd71dbf05fcd87524d3a53aa3b9696c8/components/content_settings/core/browser/host_content_settings_map.cc
[modify] https://crrev.com/8f5dd2a6fd71dbf05fcd87524d3a53aa3b9696c8/components/content_settings/core/browser/website_settings_info.h

This bug has been closed for more than 14 weeks. Removing security view restrictions.

For more details visit https://www.chromium.org/issue-tracking/autotriage - Your friendly Sheriffbot