I think unstaged window will only show changed files so that I can select which files to select for staging? I am seeing that some of the unchanged files are also in the unstaged area. I am using git repo and sourcetree user interface. This is regarding sourcetree.
You probably have changes in some non-printable characters, e.g. line breaks.
Check whether the pull down menu in the upper left corner is set to "All files". If it is, that would explain it. The usual default value "Pending files" will only show changed files.
Screen Shot 2015-03-30 at 9.16.16 AM.pngScreen Shot 2015-03-30 at 9.21.04 AM.png
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