I am using Git in VS2013 and my changed files are not showing up in the Changes window of VS.
When I have changed a file but before I have saved it to disk it does show
I had this same problem and it was happening because all the code files were in a subfolder which also contained a git repository and that was preventing it from staying in the "included changes" section after saving.
To fix it I went into the subfolder and changed all the names of the git files to something else (ex. renamed .git folder to z.git, .gitingore to z.gitingorez, ect). After that all the files showed up in the "untracked files" section and the changes stayed in the "included changes" section after saving.