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Same problem here. Just checked with a fresh jenkins installation, but symlink support with git is broken. The basic problem is that the git-client does a git init with JGit, which will create the directory and the .git/config file and add the
symlinks = false
This in turn lets the git command line client not support symlinks. So the whole point of using the git command line client instead of JGit to support symlinks is currently not working.
As regression: It seems to be a problem of JGit 3.3. Downgrading to git-client 1.6.4 (JGit 3.2) is at least not creating this core property. To downgrade, download it here: http://mirrors.jenkins-ci.org/plugins/git-client/1.6.4/ and copy it over the git-client.jpi in the plugins directory and restart jenkins.
For JGit 3.3: It is in FileRepository.java in create() method. There is a symlink check (if the OS supports symlinks) which seems to be broken. 3.2 doesn't include this check.