My Jenkins is running under the MyUser account. NOT Local System.

In my user home (c:\users\MyUser) I have a .gitconfig file with an "autocrlf = True" line.
The files check out with Linux Style ==> NOK

On a hunch, after reading the section "Configuring Jenkins to use OpenSSH bundled with msysgit Windows installer" on the Git Plugin wiki https://wiki.jenkins-ci.org/display/JENKINS/Git+Plugin, I copied the .gitconfig file to the "C:\Windows\System32\config\systemprofile" folder.
Files now check out correctly with Windows Style.

Note that I cannot reproduce the error after putting .gitconfig in "C:\Windows\System32\config\systemprofile" folder. Even if I now delete it, files are still checked out windows style, even after a fresh clone.