I mulled over this problem all night and came at it again. I have the answer. Even though your expression pedal linked to your MIDI board may be fine with other things, including the H3000se, for the Eclipse, you will need to plug your expression pedal into the back of the Eclipse and go through the 'calibrate/toe/heel' part.
Now it's 'learnt' which pedal is being used with it, when loading a new patch (with the expression pedal down/off) you shouldn't get any of the new sounds effect. You can then push your pedal forward at your own leisure to bring in the effect. (this is an expression pedal linked to a MIDI board such as The Ground Control Pro)
At the moment, I'm still using a M-Audio expression pedal, until I attain a Mission, but in theory, you may have to go through this procedure with any pedal.