As a workaround, assign the affected track to the AU-Audio Instrument DLSMusicDevice. This uses the same QuickTime synthesizer, including the ability to listen to program changes. Like any Audio Instrument, you can bounce it both realtime and offline.
Additional information
The reason this doesn't work the way you might expect is because Logic's audio engine is not actually processing QuickTime synth tracks. Instead, Logic sends MIDI data to QuickTime, and QuickTime handles the audio in parallel with Logic. Thus the tracks are not part of the bounced file.