I replied to a question by munmun a few days ago that MIGHT be the same issue.
When you use Melodyne, you need to click POST in the Inspector for the track; otherwise, Melodyne will bypass ProChannel. if this is not the question or problem, my apologies. If it is, here is the whole answer from the other thread:
Make sure you hit POST on the track. If POST is not lit up blue, Melodyne will bypass ProChannel. This gave me trouble until I figured it out.
The POST button is almost top center under the GAIN knob in the Inspector when TRACK is selected. You may have to click TRACK a second time to hide the Properties: otherwise, the POST button will be hidden underneath the Properties. Not a good design, in my opinion, but not a problem once you know where it is.