This isn't really a specific problem with this circuit. Most modulation effects have an oscillator sweep that gets up into higher frequencies than I want to hear. I built one of these a few weeks back and ran into the same thing. I always call it the, "Pennywhistle Effect." Is there a value in the circuit that can limit that? I'd love to build one of these that had a little less high-frequency wheedly-deedly. Great job with the circuit, BTW. I'm just annoying in the kind of things that get under my skin.
-Rob