Hey Tom, guess what? I might have found the answer.

Open the NOTATION window and at the top left corner you'll see a button for Opt. Click this and you're into the notation settings. Up near the top left of this window is a box labeled TRANSPOSE. If you've got anything but a zero in this box it produces exactly the problem you describe. What's worse is that the setting is preserved even after a re-boot of PT. The only way back is to change it manually.

Please let me know if this works so I can get some sleep!

ROG.