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I think I'm beginning to understand. I assume you're using the pre-scm-buildstep plugin to determine the branch to build, to create that branch, and to checkout that branch.
Does your job fail at least once if you wipe the workspace? I assume the initial workspace creation doesn't happen until after the pre-scm-buildstep, but your pre-scm-buildstep requires that the workspace exists in order to perform the checkout.
I've been able to replicate enough of your scenario to see that it fails for me as well. I created a pre-scm-buildstep shell script which performs the following commands: