I really don’t have any suspicious packages at all. And I have toggled atomic_save without any luck.
BTW below is my package list:
1Self
AdvancedNewFile
ApacheConf.tmLanguage
CodeIgniter 2 ModelController
CodeIgniter Snippets
CodeIgniter Utilities
DocBlockr
Emmet
Function Name Display
HTML-CSS-JS Prettify
HTML5
JsonTree
Legal Document Creator
Markdown Extended
MySQL Snippets
OpenPath
Package Control
phpfmt
Preferences Editor
Pretty JSON
Python 3
ShellCommand
SideBarEnhancements
Status Bar Time
SublimeCodeIntel
SublimeLinter
SublimeLinter-csslint
SublimeLinter-html-tidy
SublimeLinter-jshint
SublimeLinter-php
SublimeLinter-phplint
SublimeLinter-xmllint
Theme - Soda
Theme - SoDaReloaded
TortoiseSVN
Virtual Host Snippet
WhoCalled Function Finder