I highlighted this in a recent post.
It appears to be related to the different number of notes in the chords combined with the same note being present common to either the untransposed or transposed version of the first chord. The problem only occurs with the Shift+I popover. Using the transpose dialog seems to work fine.
In the attached examples, the highlighted notes do not transpose up or down a 2nd when the whole bar is selected, and the popover is used. The problem affects both diatonic and specific interval transposition.
