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We used the EnvInject plugin to run some tests before the repo is checked out. When building multiple configurations, there seems to be 3 git repositories, the one in the regular workspace that is checked out by the main job, and then for each configuration, another repo living in workspace/VAR/VALUE, where the project is really built.
We suspect those configuration-specific copies are not updated for some reason, and thus origin/pr/XXX/merge points to an old commit that is not present in that particular repo anymore.
We wanted to force a git fetch on those repos before the checkout, but the problem is bofore the check those repo don't even exist! It looks like jenkins do a clone for them or something.
Another weird thing is after doing this experimentation with EnvInject, the problematic PR got "fixed". We suspect that something might have been cleaned when the pre-checkout commit failed, and the checkout was never done, but all these are just wild guesses.
We'll continue to investigate this as much as possible, but all points to some conflict with multiple configuration builds.