Maybe it's just me, but I believe this is Square-Enix's fault on the re-release.
In the Shinra Mansion's basement, usually Vincent's theme will override the battle music and fanfare themes should the player have an enemy encounter. But in this new version the music stops playing altogether for the duration of the battle, and will only resume on the fanfare, then Vincent's theme will resume. Is it just me or Square-Enix screwed it up?