Ok yeah that issue isn't setup related but more related to the harmonics that are naturally created due to the reaction of the sound output. It's also likely amplified by, er...well, your amplifier. I think you can mask stuff like that with your playing style, but you can't really get rid of it. Of course, I'd really need to see it happen to know for sure if it's what I now think it is.
Here's a quick example
[YOUTUBE]YVGpfUjunvk [/YOUTUBE]