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Jenkins 1.3.3 , Git plugin 1.3.0
Got the same problem on one of three build systems running in a matrix project.
Each build slave has a different linux distro (RHEL6, SLES11, debian squeeze)
It is failing on SLES11 x86_64 and succeeds on the other two.
The target directory (work space) exists and is empty (no .git directory in it).
Workaround: remove target directory, do manual git clone into it and run the Jenkins build again. Wipe out is turned off BTW.