Does not reproduce for me on Windows.  May be Linux-specific or specific to how this distro is invoking Chrome.

+CC estade in hopes of trying to repro on Linux.

assuming I understand this bug report ("multiple instances" == multiple new windows?) I can't repro on linux either (56 or 58) but I could see an extension messing with this.

yes, multiple instances = multiple new windows. I also tought an extension could mess Chrome, but I can easily reproduce it with a 0 conf chrome dev Version 58.0.3004.3 dev (64-bit).

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ah I see, this is happening when you relaunch chrome from the desktop icon, not when you open new windows from inside Chrome (like Ctrl+N). I can repro and this does appear to be a regression or an intended change.

Oh sorry, I thought I mentioned it as comment, but it seems I forgot that this bug is not occurring with Ctrl + N.

Right, I tested with launch-from-command-line on Windows.

I don't think this is P3.  It's a regression and seems wrong, but I'm reluctant to raise to P1 since it's pretty minor.  Still, it would be good to get a bisect.

result of consolidated setup flow?

Yes, this is likely a result of consolidated startup flow.

No! The bug now affects Chrome beta since last update.

URGENT - PTAL ASAP.

We're getting VERY close to M57 Stable promotion. And 
this issue is marked as M57 stable release blocker. Pls make sure to land the fix and get it merged into the release branch ASAP so it gets enough baking time in Beta (before Stable promotion).

Know that this issue shouldn't block the release?  Remove the ReleaseBlock-Stable label or move to M58.

Thank you.

Unable to perform tool bisect since this issue is reproducible only while launching the chrome from desktop icon on Ubuntu 14.04, So providing manual bisect info below

Manual Bisect Info:
---------------------
Good build:57.0.2978.0 (442756)
Bad build: 57.0.2979.0 (443120)

CL from Omahaproxy:
--------------------
https://chromium.googlesource.com/chromium/src/+log/57.0.2978.0..57.0.2979.0?pretty=fuller&n=10000

From the above CL able to see only one change which is related to the pinned tabs.
Review-Url: https://codereview.chromium.org/2628023002

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/4349089ebb28a0509a0fc20af83c9a2c0912c3ed

commit 4349089ebb28a0509a0fc20af83c9a2c0912c3ed
Author: tmartino <tmartino@chromium.org>
Date: Mon Feb 27 19:28:24 2017

Do not show pinned tabs on multiple instances

BUG= 691781 

Review-Url: https://codereview.chromium.org/2709393006
Cr-Commit-Position: refs/heads/master@{#453294}

[modify] https://crrev.com/4349089ebb28a0509a0fc20af83c9a2c0912c3ed/chrome/browser/ui/startup/startup_tab_provider.cc
[modify] https://crrev.com/4349089ebb28a0509a0fc20af83c9a2c0912c3ed/chrome/browser/ui/startup/startup_tab_provider.h
[modify] https://crrev.com/4349089ebb28a0509a0fc20af83c9a2c0912c3ed/chrome/browser/ui/startup/startup_tab_provider_unittest.cc

[Auto-generated comment by a script] We noticed that this issue is targeted for M-57; it appears the fix may have landed after branch point, meaning a merge might be required. Please confirm if a merge is required here - if so add Merge-Request-57 label, otherwise remove Merge-TBD label. Thanks.

tmartino@ as discussed, please update the bug with Canary result tomorrow. If change looks good in Canary, I will approve merge to M57. Thank you.

Rechecked this on chrome version 58.0.3026.0 on Ubuntu 14.04. Fix is working as intended. No pinned tabs are displayed for all new instances of chrome window launched.

Adding TE-verified labels.

Thanks.!

Per #21 this is verified and ready to merge when govind@ or sherrifbot approves.

Approving merge to M57 branch 2987 based on comment #21 and #22. Please merge ASAP latest before 5:00 PM PT today so we can take it in for tomorrow's Beta release. Thank you.

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/3fbe86074cb18f42d2d090ee6ebe52d7503fa244

commit 3fbe86074cb18f42d2d090ee6ebe52d7503fa244
Author: Tommy Martino <tmartino@chromium.org>
Date: Tue Feb 28 18:40:21 2017

Do not show pinned tabs on multiple instances

BUG= 691781 

Review-Url: https://codereview.chromium.org/2709393006
Cr-Commit-Position: refs/heads/master@{#453294}
(cherry picked from commit 4349089ebb28a0509a0fc20af83c9a2c0912c3ed)

Review-Url: https://codereview.chromium.org/2719383002 .
Cr-Commit-Position: refs/branch-heads/2987@{#717}
Cr-Branched-From: ad51088c0e8776e8dcd963dbe752c4035ba6dab6-refs/heads/master@{#444943}

[modify] https://crrev.com/3fbe86074cb18f42d2d090ee6ebe52d7503fa244/chrome/browser/ui/startup/startup_tab_provider.cc
[modify] https://crrev.com/3fbe86074cb18f42d2d090ee6ebe52d7503fa244/chrome/browser/ui/startup/startup_tab_provider.h
[modify] https://crrev.com/3fbe86074cb18f42d2d090ee6ebe52d7503fa244/chrome/browser/ui/startup/startup_tab_provider_unittest.cc

Verified this issue on Ubuntu 14.04 using chrome latest M57 #57.0.2987.88 by following steps mentioned in the original comment. Observed no pinned tabs are displayed while launching the chrome for second time from desktop icon. Hence adding TE-Verified label for M-57.

Thanks!