Looks like it's an EG issue, I've talked to EarlGrey team, and they are looking at it, so I'm disabling the test for now.

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/77f7b158328aa08664baed66f8d93a029bc38f80

commit 77f7b158328aa08664baed66f8d93a029bc38f80
Author: Yuke Liao <liaoyuke@chromium.org>
Date: Fri Jul 28 01:30:13 2017

Disable testShowJavaScriptAfterNewTabAnimation on iOS 11.

This test fails on iOS 11 with the following error:

UI Test Activity:
Assertion Failure: javascript_dialog_egtest.mm:317:
Exception: GenericFailureException

Exception Name: GenericFailureException
Exception Reason: There are still alerts

Looks like it's an EG bug, and I've talked to EG team and they are 
looking at it.

Bug:  747439 
Change-Id: I2d147db4ce3dc1efd960cada46919ff9d1143559
Reviewed-on: https://chromium-review.googlesource.com/590308
Commit-Queue: Mark Cogan <marq@chromium.org>
Reviewed-by: Mark Cogan <marq@chromium.org>
Cr-Commit-Position: refs/heads/master@{#490185}
[modify] https://crrev.com/77f7b158328aa08664baed66f8d93a029bc38f80/ios/chrome/browser/ui/dialogs/javascript_dialog_egtest.mm

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/2b324b9670c04b3fc20e92f6eca4a177913aea66

commit 2b324b9670c04b3fc20e92f6eca4a177913aea66
Author: Yuke Liao <liaoyuke@chromium.org>
Date: Fri Jul 28 03:06:03 2017

Fix context menu egtests on iOS 11.

EarlGrey has a weird bug on iOS 11 when trying to match and tap a
_UIAlertControllerView using grey_ancestor. This CL fixes those broken 
tests to not use grey_ancestor, which I think also makes the helper 
function cleaner.

Bug:  747439 ,  748122 
Change-Id: I4465d7a57086e505522c3039bbe4256b5101c077
Reviewed-on: https://chromium-review.googlesource.com/590652
Reviewed-by: Eugene But <eugenebut@chromium.org>
Reviewed-by: Mike Baxley <baxley@chromium.org>
Commit-Queue: Yuke Liao <liaoyuke@chromium.org>
Cr-Commit-Position: refs/heads/master@{#490232}
[modify] https://crrev.com/2b324b9670c04b3fc20e92f6eca4a177913aea66/ios/chrome/browser/ui/dialogs/javascript_dialog_egtest.mm
[modify] https://crrev.com/2b324b9670c04b3fc20e92f6eca4a177913aea66/ios/testing/earl_grey/matchers.h
[modify] https://crrev.com/2b324b9670c04b3fc20e92f6eca4a177913aea66/ios/testing/earl_grey/matchers.mm
[modify] https://crrev.com/2b324b9670c04b3fc20e92f6eca4a177913aea66/ios/web/shell/test/context_menu_egtest.mm

The remaining test that does not pass on iOS11 is testShowJavaScriptAfterShareMenu.  This is failing because iOS11 has moved the share menu to a separate process, and we have no way to dismiss the UI once it's displayed.  For other tests that use the share menu, the recommended approach is to update the test to directly call the share menu's endpoint (e.g. circumventing the share UI to add a page directly to a reading list).  However, testShowJavaScriptAfterShareMenu is specifically testing correct JS dialog presentation after the share menu UI is displayed.  Since there are no programmatic ways to implement this test, it will remain disabled until showing/disabling the share menu via EG is supported.  This functionality is expected to be added in EarlGrey 2.0, so I'm removing the blocking status of this bug until its blocking bug has been closed.

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/200698b8d6a40f3a2e982f49400f0c212eaba5a0

commit 200698b8d6a40f3a2e982f49400f0c212eaba5a0
Author: Yuke Liao <liaoyuke@chromium.org>
Date: Tue Aug 15 20:05:04 2017

Reenable testShowJavaScriptAfterNewTabAnimation on iOS 11.

Not sure why this test fails on Xcode 9/iOS 11 beta 3, but now it works
on Xcode 9/iOS 11 beta 5, so I'm re-enabling it.

Bug:  747439 
Change-Id: I469f10596d8f8c4c47325299819780a60a353a27
Reviewed-on: https://chromium-review.googlesource.com/615046
Reviewed-by: Kurt Horimoto <kkhorimoto@chromium.org>
Commit-Queue: Kurt Horimoto <kkhorimoto@chromium.org>
Cr-Commit-Position: refs/heads/master@{#494514}
[modify] https://crrev.com/200698b8d6a40f3a2e982f49400f0c212eaba5a0/ios/chrome/browser/ui/dialogs/javascript_dialog_egtest.mm

Is this now fixed?

Test was reenabled in https://chromium-review.googlesource.com/615046; closing now.