So I came across this problem on Dropbox, but I am sure people will experience it elsewhere.
While working with a developer in India, I turned a dropbox folder into a github repo (by running git init) so I could easily diff changes done overnight. I did experience one problem though that came up randomly. One day I woke up to a bunch of modified files that apparently had no differences. When I diffed one, I got the following:
diff --git a/assets/js/jquery-ui-1.8.11.custom/development-bundle/themes/base/jq
old mode 100644
new mode 100755