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Yes, Kris is aware of this issue. It was found during Beta testing and discussed a bit. Part of the problem is that there is no way to determine where on the current screen your eyeballs are looking when you decide to flip orientation. The best any programmer could do is to assume they were on the first paragraph/sentence displayed in that view and then cause that paragraph/sentence to be at the top after rotation. Of course, that solution isn't really what you are asking for, as there will definitely be some "loss of position" after the rotation regardless.
So, I imagine, Kris put this as a lower priority than some other ideas he is working on that would actually have a solution that people will be happy with.
In the meantime, my recommendation to avoid getting caught out is to rotate the orientation at the beginning of a chapter/file. You will not lose your position because there is no "reflow error". Also, you can manually select and lock the orientation instead of letting it auto-switch. You won't ever have it switch accidentally.
Cheers!
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