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This issue still does not make sense to me.
Assuming you have:
Freestyle project A, which triggers
Matrix project B, with axis "default"
I assume the following is true after you start A:
cause of build of A: Started by user
cause of build of B: Started by A #xxx, which is started by user
cause of build of default axis of B ("B/default"): Started by B #yyy, which is started by A #xxx, which is started by user
(calling cause.getUpstreamCauses() recursively).
If so, that's entirely sensible. The build of B/default was started by the build of B, and that in turn was started by A. No build of A did start the build of B/default, the build of B did.
Note that multiple causes are generally used when a single build was started for multiple reasons, e.g. when a build, while in the queue after triggered by an SCM change, was also triggered by a user clicking "Build Now". Or a job that takes 10 minutes per build and is configured to build every minute, will have ~10 separate timer trigger causes per build.
If I'm wrong in my assumptions above, please tell me. So far everything looks like it should AFAIUI.