I think a lot of it has to do with the drastically different production. JP's guitar tones are super-clean, many of the drums are triggered and have that synthetic, dancey sound, and Moore's keyboard tones are also pretty light-sounding. Add in LaBrie's tenor voice and there's really nowhere the music sounds "dark." On Awake, Moore gets moodier, LaBrie goes into lower registers, Portnoy's kit sounds more acoustic, and most notably, JP's guitar gets a much grungier, almost industrial sound.
It was just the production of that whole hair metal era. Between IW and Awake, the music landscape changed a lot, and that was no longer in fashion, so the producers tried to portray DT as a moodier band to fit in with the trends.