A lot of phase issues can be traced to using digital effects in a parallel loop. This can certainly cause a loss of treble and/or bass, depending on the effect and the settings used. If you're using the MF in a parallel loop, try setting the loop mix to 100% (basically turning it into a series loop) or try turning DRYKILL on (one or the other, but not both at once). Either should help get rid of any phase issues. You might try using the pedal in front of the amp, too (DRYKILL should be off in this case).
If you have bypass set to relay (true bypass), you may notice a difference in tone when the pedal is on. You might try DSP bypass, which will make active and bypass more similar in tone.
Can you give us some more details about your specific setup? Knowing what is plugged into what and how it's plugged in might help us to come up with some suggestions.
