Yes, although it varies from soundtrack to soundtrack. My Atelier Iris soundtracks (both 1 and 2) are louder than a lot of music around them, so I tend to leave them off of shuffle playlists for that reason. Some of the recent releases of NES music (the Kunio boxset is the main offender) also exhibits this trait/flaw and to be honest, is more than a little fatiguing. Also, the Master System PSG from the Fantasy Zone boxset, which I recently encountered (the arcade/FM stuff is fine for me though). I can't say I noticed it on FFVI, but definitely on the Ys Renewal albums (I tend to favor the PC-88 originals, they don't sound as bright as the Renewal discs, especially for Ys II).
I'm not 100% sure, but I'm assuming there's a peak around 2khz and 4khz on some of those recordings and the replaygain "normalizes" it but still leaves that peak in place. I would also assume that, even though an orchestra operates in that frequency range, the sounds aren't as harsh and is also more spread out throughout the track overall. Our ears are very sensitive to those 2khz-4khz frequencies, so my guess is they sound louder. I think I might try taking some of them down another decibel than usual to see if it helps.
