I keep winamp around for various reasons like plugin comparisons. Anyways I noticed an issue when comparing how Metroid Fusion sounded compared to real hardware, Caitsith2's gsf plugin and 3.0.2 of your plugin.
From foo_gsf: https://www.dropbox.com/s/bzi1j6bd9tkdjd2/VS.%20Fake%20Chozo%20Statue.mp3?dl=1
A real hardware video: https://www.youtube.com/watch?v=0XYXu8i1de4&t=11m52s
@kode54 plenty of people still use Windows Media Player mostly because of familiarity and it's probably one of the easiest to use, at least for me but you're right. There are other great players like XMPlay which I recommend.
The gsfs use the original files played back through emulation. If the gsf's were ripped properly and the emulator is accurate, then the gsf's will sound like what they were supposed to sound like.
The midi's and soundfont were transcribed, in a sense. This can have issues if the program doing the transcribing doesn't 100 percent understand the game's sound driver and format as is the case with this game. Also, if the game uses the gameboy's sound hardware in any way, that feature can only be simulated with pre-recorded sounds in the soundfont rather than emulated and may end up sounding off as a result. "VS Fake Chozo Statue" is one of those tracks with this kind of problem.
Maybe you can upload just the GSFLIB/MINIGSF files? Conversion output is kind of redundant since I have the software to generate the same audio.
E: Here's a GBA ROM from the affected GSF:
https://f.losno.co/chozo_statue.zip
Compare against hardware, please. Yes, I know it's somewhat wrong now, but it sounded closer before. Highly Advanced is in no way a proper reference anyway, it was never volume level accurate between the GB and GBA sound.
Oh, and this isn't the wave channel, it's not even being used here. Just the two square wave channels.
edited 9:45 PM EDT September 3, 2017
E: Here's a GSF (or minigsf) to GBA converter, it imports all the MINIGSF/GSFLIB chain to produce the final GBA ROM that the emulator runs.
I know highly advanced has issues, but the 2 square wave channels still sounded similar to the video I posted several posts back... plus it was either use that as a comparison, the soundtrack version, or viogsf.
The gsf's I'm using are the ones that I think you posted awhile back. They're probably up on gsf.joshw.info now as a replacement for the old set.
This might be a better video for comparison, but it's still just as noisy: https://www.youtube.com/watch?v=yB7oSrPGAag&t=5m00s