Not seeing that problem here. But maybe I don’t understand. (e.g., there is no tool called the “midi transpose tool”)
Try this in a new, empty project to investigate:
- Create one midi track
- Create one midi part
- Open the part in the Key Editor, add a bunch of notes
- Close Key Editor
- With the Select tool, click on the midi part to select it.
- Open Transpose Setup… from the MIDI menu
- Set Semitones to -12, and make sure nothing else is activated in that dialog.
- Hit OK
What happens?