[Darryl Ramm]

The simple mistake that might cause problems like this is to make both clicks on the same note duration and then the monophonic nature of the plugin bites you, if Click I and II are on the same note duration and you pull down the volume all the way on Click I it's silence on that click suppresses the click that Click II would make.

Is the Click II light blinking for the clicks you can't hear?

Besides that try trashing prefs, starting with a new empty session, and posting screenshots of exactly what you are doing (e.g. showing if you are following a tempo track or not, actual click sounds selected, clicks are on what note duration etc.).