I guess you are using a bit of metalizer in your sound.
Metalizer is a very sensitive circuit, On the pot range they are some points, especially at the beginning of the range, where metalizer sound can indeed be affected by the LFO, even if LFO amount is at center position. Being extremely sensible to power supply voltage variations, is one of the drawback of this circuit....
If you use a larger amount of metalizer, it should not be noticeable anymore.