I've figured out that this is a bug that specifically affects Utility tracks, and only when using an external MIDI device instead of a VSTi/DXi plugin, and have created a bug report for it. To duplicate it, set BB to use an external MIDI instrument (either hardware MIDI or the Microsoft GS Wavetable synth), then add any RealTrack with notation to a Utility Track.
The workaround for the moment is to use a VSTi/DXi plugin as your default synth, or to avoid using the Utility Tracks.