I was encoutenring alternate tuning problems as described in previous threads : http://line6.com/support/thread/81532?tstart=0,
Typicaly with DADGAD Tuning , T-model , position 3
I opened the back plate of my Korean JTV : by dampening the 3 springs with the fingers, the problem vanished.
By close looking at the springs, they had inside a folded foam tape strip (see picture). As the guitar is a first hand one, theses strips were intentionaly inserted by Line 6 in the springs for noise reducing, I suppose
Unfortunately for me , they did not correctly the job
I chose to insert inside each spring a small rubber tube : The noise have so far disappeared, but don't know how long it will last
Anyway , my personnal analysis is : No use to spend time with reflashing , intonation fine tuning , etc, : Check (or have it checked by your dealer) the hardware
Hope it could help some of you