The mouse drivers are probably sending multiple scrollwheel events per wheel click.
Check that SetPoint does not have any application overrides which might mean your mouse settings changes were ignored.
You may also need to fully exit Opus & restart it after changing the mouse control panel as some of the settings may be cached when Opus starts.
That said, my SetPoint settings also use 3 lines, and Opus only scrolls one column per click of the wheel in List mode:
It's possible that Windows 8's own mouse control panel has some effect in addition to, or instead of, the Logitech one.