Executing pane:close will ask to save changes of TextEditors twice

Prerequisites

• Can you reproduce the problem in safe mode?
• Are you running the latest version of Atom?
• Did you check the debugging guide?
• Did you check the FAQs on Discuss?
• Are you reporting to the correct repository?
• Did you perform a cursory search to see if your bug or enhancement is already reported?

For more information on how to write a good bug report or enhancement request, see the CONTRIBUTING guide.

Description

If you execute pane:close the dialog asking you to save appears twice when you press the Dont Save button. This does not happen with core:close command in combination with the Close Empty Panes configuration option.

Steps to Reproduce

1. Open Atom in safe mode.
2. Ensure you only have one pane, this bug does not reproduce when closing a split pane.
3. Open a new untitled tab (Or any tab it is not limited to untitled tabs).
4. Make any modifications to the tab.
5. Run pane:close from the command-palette, this doesn't reproduce when the pane is closed using the Remove Empty Panes option.
6. In the dialog that appears press Don't Save.

Expected behavior: Pane to close.

Actual behavior: Dialog asking to save appears once again.

Versions

atom --version

Atom    : 1.12.0-beta0
Electron: 1.3.6
Chrome  : 52.0.2743.82
Node    : 6.3.0

apm --version

apm  1.12.5
npm  3.10.5
node 4.4.5
python 2.7.11
git 2.10.1.windows.1
visual studio 2015