I'm going to try some more experiments with different computers and setups this weekend, to see if the clean/effected sound issue is isolated to the Helix Native plugin or not, but so far it appears to be.
I'm starting to think this might be a bug, or some type of incompatibility between the plugin and the sonic port vx. I know the Line6 dev's don't have a lot of time to read the forums and answer questions, so I will continue to keep "plugging" away at this.;-)
If anyone has any ideas or thoughts on how to troubleshoot or isolate this, I'd really appreciate your input. Thank you.