First off, welcome to the Bluebeam Brainery, we all appreciate what you have to contribute to making all of us better. If anyone is ever NOT easy on you, let me know, they are not a culture fit for the group.
It sounds to me like you tried everything to confirm the bug. Sometimes users will use the Rotate tool rather than the Rotate Pages tool. This can result in all the pages looking correct, but how the markups associated with the page are still rotated. Think of it as a coordinate system on paper. Like I said, it sounds like you checked everything, I just wanted to bring this up, just in case.
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