I work on Mac OS, but to date this problem has only occurred on my MacBook Air with an SSD hard drive. I do a fresh checkout of a number of different repos and status
shows me a long list of modified files (without touching anything). It seems to be third party javascript and css files. That with what else I've read seems to be line endings, but despot setting:
git config --global core.autocrlf input
As suggested here http://help.github.com/line-endings/ and then checking out. Has the same problem.
Help =(