I created a matrix project, using the repo SCM (RepoSCM). The main job correctly syncs the source into the main workspace area. The sub-jobs incorrectly also sync the source into the main workspace, rather than the per-configuration workspace.

Console output from the main job:

Building in workspace /var/lib/jenkins/jobs/repo-matrix-failure-bug/workspace
[workspace] $ /home/swarren/shared/git_wa/swarren-home/bin-swarren/repo init -u git://github.com/NVIDIA/tegra-uboot-flasher-manifests.git -g default,-tools,-bootloader
...
repo has been initialized in /var/lib/jenkins/jobs/repo-matrix-failure-bug/workspace

Console output from the sub-job:

Building in workspace /var/lib/jenkins/jobs/repo-matrix-failure-bug/workspace/board/harmony
[harmony] $ /home/swarren/shared/git_wa/swarren-home/bin-swarren/repo init -u git://github.com/NVIDIA/tegra-uboot-flasher-manifests.git -g default,-tools,-bootloader

repo has been initialized in /var/lib/jenkins/jobs/repo-matrix-failure-bug/workspace

I'm attaching the job configuration XML file too, which should "just work" in a standalone fashion.