Yeah, given that it is not easily reproducible, and only appears in one specific context, I think opening a case with Microsoft is the right way. Particularly when you cannot share the code publicly. Microsoft will most likely require to get copy of a the code or the database, but that's a completely different level of confidentiality. From what you say, it smells like a bug.

If you would find the time to report back when the issue have been resolved, I would appreciate it!