Here is my Settings - User config:
Settings - User
{ \"auto_indent\": true, \"color_scheme\": \"Packages/Color Scheme - Default/Twilight.tmTheme\",
The comment states
// Determines what character(s) are used to terminate each line in new files. // Valid values are 'system' (whatever the OS uses), 'windows' (CRLF) and // 'unix' (LF only).
You are setting
"default_line_ending": "LF",
You should set
"default_line_ending": "unix",