Strange, the stock Rat circuit doesn't flip the polarity, and its single-pole treble pre-emphasis shouldn't require the polarity to be flipped relative to the clean blend (as would be required in a two-pole design). Perhaps if the clean blend is not properly low-passed you may be hearing comb-filtering weirdness in the treble. I don't have experience with this particular pedal (the MXR), but interested to hear what comes of this discussion.
