A LOT of effects boxes (especially the cheaper ones) screw up your tone when on "standby" or "bypass." I don't know why it's so hard to bypass a pedal without screwing the tone up (adding treble seems to be the most common side-affect).

I went so far as using a separate mixer to bring effects in (reverb, echos, etc). I don't "bypass" these effects, I just shut them off. The dry sound comes into the mixer in its own channel, so there's nothing to color it.

You can only do this with additive effects, though--the digital whammy is a pitch shifter, so there IS no dry tone. Pitch shifters tend to make the bottom end go away if they aren't real good--that's why it sounds more trebly. No bass.

I'd skip the effect entirely--how often will you use it? Why screw up your tone 98% of the time for an effect you'll only use 2% of the time?