Don't quite understnd what you are saying. But, my guess is that you are mixing a dry signal with the output of the unit, whether by use of the wet/dry control or externally.
Any digital unit has a small time delay, usually caused by both the conversion process and internal buffering. This means that if you mix the output of the box with the dry input, you will get a"comb filter" effect, which can sound like phasing.
The only way to avoid this is to not mix the output with a dry signal when in a bypass state, or when using a simple effect. This applies to all digital units, not just ours. You say that you have set the bypass to mute -my guess is that audio is still getting through – make sure that the various wet/dry settings are set to 100% wet.
