Create multiple patterns with notes in them. Right-click in the pattern editor, choose “Track->Transpose -12” and you’ll see the notes in the current pattern transposed down – all other patterns are unaffected.
I thought perhaps it was a setting in the advanced editor (which I would not expect to have an effect on this menu command anyway). I changed the advanced editor to “track in song,” and the right-click command still did not work. Transposing from the advanced editor worked fine.
I did not try up/down 1, or up 12 to see if they were broken too. Just down 12.