Watch the video. I'm using three rigs. The first is just a standard rig. Nothing fancy, just a few chords leading into the lead section of Heart's "Straight On." The second and third take advantage of the pitch shifting in the KPA. I'm switching using the Kemper's buttons rather than a footswitch so you can clearly see when the changes occur.
The problem: When I get to the third rig in the sequence, I am using a highly customized user scale so that I can harmonize the correct notes over all those chord changes. The first run through the part played using the final rig has some bad harmony. I play it again immediately afterward to demonstrate the problem...which is this - I think the KPA needs a little time to load my user scale. The second time I play it, the rig has been loaded for a while and the harmony comes out perfectly. The first time, you can hear it getting "confused" at first, as to which notes it should be harmonizing on top of the single note line I'm playing.
Any help is greatly appreciated.