Git changes not showing in VS2013 Update 2

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 up. But as soon as I save the file to disk the change disappears from the Changes window. I tried uninstalling and reinstalling VS2013 but it did not help. Any ideas on how to keep the changes in the window once they are saved? I have been using Git on the command line to work around this issue so that git client is able to detect that there are changes. Before save. After saving file change disappears.