I am a new Variax (59) and HD500X user. I bought the variax mostly for the guitar emulations and alternate tunings. All the alternate tunings sounded pretty good in the store. When I got the Variax set up at home, it was at ver 1.7. I updated it to the current version (2.0), and now I have the same problem you have described. Pretty much makes any alternate tuning it happens on useless. Absolutely can't have the original non-altered notes bleeding through. In my case it is definately NOT the acoustic sound of the strings, the original notes are being amplified through the system somehow.
I barely know how to use the Variax workbench yet, but I tried to check if the "Mag Pickup Blend" feature was somehow getting turned on for the alternate tunings, but so far I haven't found that to be the case, but as I said, I don't know my way around that piece of software yet.
You are definately not alone on this problem, and I am really looking for a resolution to this as the alternate tunings are important to me. Hope someone finds an answer, or it turns out to be a glitch that gets fixed in an update soon. The "Mag Pickup Blend" is a great feature as it adds a little more realism to the modelled emulations, but absolutely should not happen if using an alternate tuning.