Repro:
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Click on ARC shortcut and app in shelf. Spinning animation is started on both. That is expected.
ARC booted.
ARC app is launched. However not shortcut.

It expected that shortcut is also stated on ARC boot

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/58df084dd54feed0de177c707cb26b004c05cf68

commit 58df084dd54feed0de177c707cb26b004c05cf68
Author: khmel <khmel@chromium.org>
Date: Thu Apr 06 02:05:05 2017

arc: Make shortcuts runnable in deferred mode.

BUG= 708792 
BUG=b/36990317
TEST=Manually, unit_tests extended

Review-Url: https://codereview.chromium.org/2799813003
Cr-Commit-Position: refs/heads/master@{#462324}

[modify] https://crrev.com/58df084dd54feed0de177c707cb26b004c05cf68/chrome/browser/ui/app_list/arc/arc_app_list_prefs.cc
[modify] https://crrev.com/58df084dd54feed0de177c707cb26b004c05cf68/chrome/browser/ui/app_list/arc/arc_app_list_prefs.h
[modify] https://crrev.com/58df084dd54feed0de177c707cb26b004c05cf68/chrome/browser/ui/app_list/arc/arc_app_unittest.cc
[modify] https://crrev.com/58df084dd54feed0de177c707cb26b004c05cf68/chrome/browser/ui/ash/launcher/chrome_launcher_controller_impl_unittest.cc

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/0d3abca72d754f20e75bab1504c511e1c4bab3e5

commit 0d3abca72d754f20e75bab1504c511e1c4bab3e5
Author: khmel <khmel@chromium.org>
Date: Thu Apr 06 21:37:37 2017

[Merge M58] arg: Make shortcuts runnable in deferred mode.

TBR=xiyuan@chromium.org,msw@chromium.org
NOTRY=true
NOPRESUBMIT=true

BUG= 708792 
BUG=b/36990317
TEST=Manually, unit_tests extended

Review-Url: https://codereview.chromium.org/2799813003
Cr-Commit-Position: refs/heads/master@{#462324}
(cherry picked from commit 58df084dd54feed0de177c707cb26b004c05cf68)

Review-Url: https://codereview.chromium.org/2807483002
Cr-Commit-Position: refs/branch-heads/3029@{#614}
Cr-Branched-From: 939b32ee5ba05c396eef3fd992822fcca9a2e262-refs/heads/master@{#454471}

[modify] https://crrev.com/0d3abca72d754f20e75bab1504c511e1c4bab3e5/chrome/browser/ui/app_list/arc/arc_app_list_prefs.cc
[modify] https://crrev.com/0d3abca72d754f20e75bab1504c511e1c4bab3e5/chrome/browser/ui/app_list/arc/arc_app_list_prefs.h
[modify] https://crrev.com/0d3abca72d754f20e75bab1504c511e1c4bab3e5/chrome/browser/ui/app_list/arc/arc_app_unittest.cc
[modify] https://crrev.com/0d3abca72d754f20e75bab1504c511e1c4bab3e5/chrome/browser/ui/ash/launcher/chrome_launcher_controller_impl_unittest.cc

Trying to verify this issue, please let me know where to find shortcut option. Thanks!!

Verified on 9557.0.0, 60.0.3101.0 using test app in https://bugs.chromium.org/p/chromium/issues/detail?id=717661#c7