UPDATE This may have been a Vim issue for me. After modifying a file and saving in Win32 Vim, the filemode was changed and git would say there was a change. See :help backupcopy in vim for more info. The fix is to add this to your .vimrc:
:set backupcopy=yes
If something else causes this that you can't control, you can tell git to ignore these changes with this:
git repo-config core.fileMode false