I have had exactly the same experience as you with the levels getting all screwed up. I go to the mixer and adjust the harmony level higher and the volume goes completely away. My suspicion is that as we increase the volume of the harmony voice we are telling the effect processor #4 something it doesn't like to see. If you notice, the effect is usually on a noise gate or limiter effect and I think this could have an affect on the levels. I have to spend more time with this. Now, if you want a really good vocal harmonizer, I've just had a ball today installing and playing with the Solton X1 vocal harmonizer. It's the best on of used yet! The sound is stunning, the levels perfect and it does everything I want a harmony box to do.
George Kaye