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I created a unit test that reproduces the problem, and created a fix. Both are available with this pull request: https://github.com/jenkinsci/git-plugin/pull/235
The fix does not modify the behavior for regular projects, or matrix projects that do not use the git pre-merge feature.
The current implementation always uses the decorated revision for the matrix axes. However, the decorated revision only exists in the workspace of the cloned parent build, and does not exist in the cloned workspace for the axes. This fix causes the axes to use the marked revision, rather than the decorated one. The axes then subsequently decorate the marked revision.
The only other way that I could think of fixing this problem would require the axes to pull the decorated revision from the parent workspace. However, this would cause all kinds of headaches in particular if working with multiple distributed slaves.