Problem changing patches with the midi mate

I just got my AxeFX this week and I'm loving it!!

However, I've come across a small problem..

I'm using a midi mate in controller mode to changes patches and turn on/off different effects. For some reason, when I change patches with the midi mate all the effects are bypassed by default. However, if I change the patches with the 'wheel' on the front of the axefx, the effects are 'on' by default (which is what I want).

Any ideas how I can change patches with the midi mate and select what effects will be on by default (ie. drive1 + delay + reverb)
 
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