I'm having the same "ghost note" problem on my Korean JTV-59 with FW 2.0.
The altered tunings worked correctly when I got the guitar with FW 1.8. They still worked correctly after I applied the FW 2.0 update.
Then I edited one of the tunings, per the procedure in the manual, and saved it to the guitar.
Now, all of the tunings (including factory ones that I didn't change) pass both the altered pitch and the natural string pitch. Essentially, changing one tuning broke all of them. This occurs on all guitar models.
Here's an example of what happens:
I select a tuning that lowers the 1st (high E) string to D (e.g., BLUES G). When I pluck the string, I hear both D (the altered pitch) and E (the actual string pitch) in the headphones or amplifier. If I go into Workbench HD and lower the volume of the 1st string in the tuning window, both notes decrease in volume. It's hard to tell for sure, but it sounds like both notes are being processed by the guitar model.
The 1st string in the procedure above is just an example.
The problem happens on any string that is altered by a tuning, on any guitar model.
It occurs regardless of whether the guitar is connected to the computer.
POD presets are not a factor. I do not own a POD with a Variax port. I'm using the USB to MIDI adapter that came with the guitar.
The mag pickups are not mixed in.
I am not hearing the strings vibrating on the guitar.
The altered tunings are no longer suppressing the actual string pitch.
I hope they find a fix for this soon. The tuning function is one of the main reasons that I bought the Variax.