Do you still have the clicking noises in the same places after you stop moving the EQ controls? If not, i wouldn't worry about it. It's probably your processor not being able to keep up with the effect changes in real time. It might also be the occasional time when the change is large enough that the waveform suddenly makes a large jump from one sample to the next because the succeeding sample carries the newest EQ change while the preceeding sample does not.