Hmm, I see... I'm running out of ideas. You might be right with your assumption about a bug in the Beam Flink runner. In this case, this would be an issue for the Beam project which hosts the Flink runner. But it might also be an issue on the Flink side.
Maybe Aljoscha (in CC), one of the authors of the Flink runner and a Beam+Flink committer, can help to identify the issue. Best, Fabian