Hello, I read all your posts and can confirm my guitar has EXACTLY the same symptoms as yours after upgrade to 2.0. I tried reflashiÃng back to 1.9 and to 2.0 again, but with the same result. Obviously there is a bug in firmware showing on some guitars only.
I have exactly the same problem as The_Doc_Rock - guitar sounds thin, ugly after upgrade. I have brand new, Korean JTV-69 so this behavior is probably not specific for certain model/production batch.