This is just something i bumped in too.
A friend of me just encoded a track for me and transferred it to my server. I listened to it immediatly and was almost blasted away on my headphones because he didn't replaygain the track.
So the first thing i did was fireing up replaygain. Replaygain started calculating and stopped with the message 'not a mpc sv7' (or something like that), so i checked the file info dialog in winamp and saw 'streamversion 7'. I also saw that the file was tagged with id3v1.1, and then i remembered he always uses id3v2 also (with mp3 that is).
I used 'tag' to remove the tag and indeed it was tagged with id3v1.1 & id3v2. After that i could replaygain the track without problems. Problem probably comes from the fact that id3v2 sits before the rest of the data ?
And just out of curiousity the other way around: Is the replaygain data overwritten when you add an id3v2 tag ? I can't check this because i don't have an id3v2 tagger (and i don't want one also !).