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I don't understand that description. You say that you're using the credentials plugin, but also say that you're using a private key from $JENKINS_HOME/.ssh/. Are you using that private key by defining $JENKINS_HOME/.ssh/id_rsa as the source file for the private key in the credentials definition, or are you relying on the default behavior of command line git that it will find that private key if run on the master node?
Another alternative you could test would be to see if the same behavior happens if you use JGit as the git implementation. You can enable JGit through the system configuration by adding a git implementation, then choose JGit. That will enable a drop down in the job which will let you change between "git" and "jgit" as the implementation.