Edit: Hmm, not seeing (well, hearing) this. Just tested and the game does indeed stay muted if you have it muted in windows. It will obviously change it if you "muted" the audio by just taking the in-game slider to zero, but don't mess with those! Adjust the volume in the Windows mixer.
Yup, that's intentional. Audio balance is tricky in RPG Maker: you have global volume, and then song volume within that. Once you start in on a certain level globally, you're kind of stuck with it, because everything is tuned to that level. If you find out it doesn't give you enough range for a track, you're screwed, and amping or de-amping a song in a separate editor has its own issues.. So I manually tweak the overall volume output for the game on certain songs to bring them up or down to where they need to be. Not elegant, but it works for the main use case. Sorry for anyone who had it muted and got blasted though. Odd that I haven't run across this myself, as I often have it muted while playtesting certain things, and I could have sworn some of that involved the boss fight.