.
.
I think that's the nature of the beast in this one. The originals had the same deal going on with the bottom of the sweep having the most dramatic "de-tuning" portion. In general if you dial it out the flange doesn't sound as thick. The less regeneration you use the less of that effect you'll get. I tend to set mine up with a very slow sweep, no regen, and low width setting but I'm not looking for an effected sound as much as a tone change and it fattens up the guitar signal a bit.
.