The latest reply from Line 6 which at last seems to admit the problem is on of the electronics not being able to cope,
We’ve spent several hours investigating this. Our QA dept. was able to reproduce the issue exactly as recorded and reviewed the use case w/ engineering.
The following are the conditions which combine to produce the issue:
• For every open string on the guitar, there are several fretted notes on other strings which due to their harmonic relationship will excite a sympathetic vibration in the appropriate open string.
• Piezos pick up harmonics and also quiet fundamentals a bit louder than mags do both due to the difference in how they convert the strings energy to electricity AND their placement exactly at the bridge’s break point. We do quite a lot in F/W to compensate for this and model the sound and behavior of magnetic pickups, but some aspects of the piezo do still have a slight effect on the end sonic product.
• When the user plays a note that excites an open string, and either the played or sympathetically excited string is virtually retuned down a step, the interval which would normally be a unison (in the case the customer originally described) becomes a Major 2nd which is comparatively dissonant.
This is very simple to confirm. The same sound in the issue can be easily produced by (in variax mode w/ the blues G tuning) playing a twelfth fret harmonic on the G string (even very quietly) and then playing the offending note at the 3rd fret on the highest string (physically a G, but sounds as an F due to the virtual tuning). Not to point out further problems, but playing the 5th fret on the B string (in blues G) will produce similar results if the A string is not muted for exactly the same reason.
While this behavior is arguably less than optimal since this differs from the behavior of a guitar which has actually been retuned, it is currently a limitation of our system. Attempting to determine in real time w/ out added lag whether a specific harmonic was picked, tapped, lightly touched to convert from a sustaining fundamental or excited sympathetically is highly complex and as no such technology is implemented in any current product may not even be feasible.
For the short term the way to work around the issue (while using virtual tuning) is to focus on right and left hand muting of individual strings while playing as one would in a high feedback situation such as playing a hollowbody at a high stage volume.
Another solution is to actually physically retune the guitar, though this is understandably unacceptable in a stage setting if the guitar is to be played in multiple tunings during the same performance.