Simply make sure to type (once), before the next checkout:
git config --global core.autocrlf false
That will avoid the kind of automatic eol (end-of-line) transformation that this setting (set to true by default with msysgit) does.
.gitattributes
files are a better place to declare the files you want to have their eol managed.
See "git replacing LF with CRLF" for more on that setting.