[Plugin: Chords and Lyrics] Chords at end of lines are positioned lower

Also, how can one switch from three-column to two-column display?

Yep, this is a known issue. I believe that it can be fixed with CSS by vertically aligning the td elements to the top. What is happening is that normally a chord and a lyrics are displayed within a table cell (td) over/under each other with an intervening br. When a chord appears at the end of a line without a lyric, the chord gets aligned to the vertical center.
I’ll check into fixing it in code also.

I’ve just uploaded version 1.6.
This release fixes the end of line issues reported. It also improves the handling of big chords over little words and other difficult situations.
I’ve removed the experimental multipage formatting.
Note that the control to select lyrics-only display has been moved to a section at the bottom of the Settings->Reading page.
I have also tested with WordPress 3.0 release candidate.