One thing that can cause a Scripture reference to be underlined is when it becomes a link by clicking the Link all References on Page button. It will make the link live and cause a popup on mouseover. Is this what you mean? The only other way to underline is with the text underline button.
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But to him that worketh not, but believeth on him that justifieth the ungodly, his faith is counted for righteousness. (Rom 4:5 AV)