Moving the cctbx_project directory to cctbx_project.old forced svn to get the latest version from scratch so buildbot at LBL has no versioning issues like Jenkins at Diamond does. Further, svn update on my local sources got the latest version, so I'm inclined to agree with Markus that that's a Jenkins issue.
I installed git on the build nodes at LBL to accommodate the changes to bootstrap.py, however reconfig.sh still fails. This new line from r22623 and r22626 is the culprit:
git_available = self.shell(command=['git', '--version'], haltOnFailure=False, quiet=True, silent=True).run() == 0
While this clearly works on Jenkins, when ran by buildbot, self.shell() is returning a buildbot shell object instead of a Builder shell object, so the .run call fails (not implemented).
I'm out of time until this afternoon to look deeper. I've left the build bot server running using r22622 of bootstrap.py for now.
-Aaron