Apparently much of the problems stemmed from the violinist and bassists' deeply held beliefs. They increasingly had a problem with the horror imagery which dominated the band's songs. Vocalist Steven Juliano commented in a recent interview:
I was raised a Catholic and I believe in God, but we're not a Christian band, They were devoted Christians, to where they were telling people in interviews that we were a Christian band. It really became a problem when we were recording the record. Kerith would be sitting there with a highlighter, going over the lyrics to highlight things that she didn't like. It was like the Nazis in World War II, like 'I'm going to tell you what you can listen to, and what you can't listen to.'
She didn't even want me swearing on-stage, It's not like I have any desire to get up there and be a potty mouth. But I remember one time I said 'Fuck' and she cried in the tour van for a half-hour afterwards.
You can find the rest of the interview via straight.com.