First off, how were you able to adjust the 'Q' of the areas you manipulated? The 'Q' of the actual sound may vary a great deal from the 'Q' of your EQ device! And usually the EQ device is the one failing to have as tight a 'Q' as the real world speaker. So (at least guessing) when you adjusted the system you were not just dropping the actual peaks, but dragging down a broad range of frequencies nearby.
That might explain the general leaness of your results.
One way to alleviate would be boost around the peak instead of dropping the peaks. leave the peaks up, and bring up the rest of the sound. That way you are not as caught by the failure to limit 'Q' as much . (at least I think it might work better)
(If anyone is confused by what 'Q' is, the Q is the curve of the slope. A tighter Q is a narrower and thinner slope to the peak of the change. A low Q is a broader wider range across the frequency spectrum.Failure to control Q is probably the worst feature of many equalizers.