I too have experienced this issue. I would recommend making the scaled percentage editable in the text frame panel, making the newly created text frame scaled to the same percentage, or removing the threading option when you scale a frame with the detached handle (essential converting it to art text). It's not a "bug" as we've been told, but it makes no intuitive sense whatsoever. It's easily solved by creating new text boxes, but this seems to be just an oversight on the devs team when considering the usability of this tool combination. Looking forward to a solution.
On the plus, I think I'm close to abandoning Adobe entirely. woot woot