My prayers were answered and I have now recieved help fixing the channel 3 playback library bug. My greatest appreciation goes to Dave Murphy (WinterMute) for doing this. This version includes a modified tracker EXE which aligns the channel 3 waveforms properly in its .BGF file output. That together with a change in the order in which the bit flags for controlling channel 3 are set, have brought BoyScout to a final version 1.0 milestone.
Please download the latest v.1.0 distribution from the downloads section.
I'd also like to direct people to WinterMute's devkitPro page, which includes a library called libagb that now contains the fixed BoyScout playback routines. In the project's CVS is also a compiling example of BoyScout playback.