I think Gidman has your answer.
If the track is clipped before you apply the EQ, lowering the setting will not get rid of the clip. It'll just make the volume lower.
If it's not clipped before you apply the EQ, than the problem is most likely that adding in the effect is starting to tax your system resources.
I think the resource that is most taxed by realtime FX is your RAM. However, maybe someone else may want to comment on that further.