I don't think anyone currently in the band dislikes "Silent Tomorrow". Eric wasn't fond of what it turned out as, since he had a different vision of what the song should be when he first played it for us and we Doom-ed it up, haha.
Both "Silent Tomorrow" and "Harmony Divine" are songs that we like well enough, but when it comes to performing them live it's just a matter of what fits best with the other songs we're playing and so on. "Silent Tomorrow" as discussed before is a difficult one due to the strong keyboard presence, and "Harmony Divine" was played consistently for two or three years in our sets, and ultimately just had to make way for newer material that translated better onstage than that song.
Like Paul said, when the time comes that we do the DVD performance, we'll try to perform as many songs from throughout our catalog as possible, maybe even something from "Amid its Hallowed Mirth"! But as for our usual sets (which rarely allows us more than 35 minutes to play), we just prefer to play the newer material that, I feel, works much better in a live environment anyhow.