Thanks for the suggestion. It turned out the problem wasn't the PF, the effects loop setting on my amp must have gotten bumped and was set to run the loop in parallel. That explains why I was hearing the original signal with the harmony. I switched it back to run in series and it's fine now.
I do hope there is a software update soon to make the tracking better for the diatonic effect, When playing duel guitar harmonies, if you play faster leads the harmony notes are kind of slurry & wobbly.