I do not know any Jenkins(user only) but I have an feeling some of the issue is located in MultiJobBuilder.java. I believe the build number gathered with project.getLastBuild() could be incorrect if sub build is allowed to execute parallel. Is it possible to query project(sub build) about upstream build number to make sure the correct sub build number is used?

[...]
        public boolean perform(AbstractBuild<?, ?> build, Launcher launcher,
                        BuildListener listener) throws InterruptedException, IOException {
[...]
                                                addSubBuild(thisBuild, thisProject,
                                                                (AbstractBuild) project.getLastBuild());
                                                projectList.remove(project);
                                                futuresList.remove(future);
                                                break;
                                        } catch (ExecutionException e) {
                                                failed = true;
                                        }
                                } else if (project.isBuilding()) {
                                        addSubBuild(thisBuild, thisProject,
                                                        (AbstractBuild) project.getLastBuild());
                                }
[...]

I may very well wrong!

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