Winamp's newish replaygain support is based on reading and writing replaygain info in id3v2 tags. It doesn't recognize APEv2 tags, nor does mp3gain recognize Winamp's replaygain tags.
This could result in a situation where two differing sets of replaygain tags are on a file, because it was first scanned in Winamp or another id3v2 program, and then adjusted in mp3gain.
Would it be possible to include the option of id3v2 reading/writing abilities to mp3gain, and the ability to turn off APEv2 tags?
That's exactly what I just wanted to suggest.
WinAmp shows/uses id3v2 tags for Track and Album volume and I think mp3gain should update this data.