Wrong pitches displayed for chords with accidentals, even for non-transposing instruments

Windows 7, GIT commit: a722cfd

There are a few different aspects to this that seem related enough that I am going to report them all together here.

1) new score for flute (a non-transposing instrument), C major
2) note entry mode
3) enter A, down, Shift+C, up - result is chord containing Ab & C#, as expected
4) exit note input mode
5) select all
6) Ctrl+Up

Result: chord moves up an octave, but accidentals disappear. Pitches still play correctly. Toggle Concert Pitch and the accidentals reappear (and stay visible as you continue to toggle).

Another way to see this:

1) same score; select all, delete
2) note entry mode
3) enter A, Ctrl+Up, down, Shift+C

Result: the flat on the A disappears as soon as you enter the C

The following was the first observed symptom of what I assume is the same bug:

1) same score; select all, deletew
2) note entry mode
3) A, Ctrl+Up, Shift+C - result is chord of A & C above staff, as expected
4) exit note entry mode
5) select all
6) click sharp icon on toolbar, result is sharp applied to both notes, as expected
7) save
8) close
9) reload

Result: chord now displays as F# & A. The A plays as A#, the F# plays as C#.