I have been following, and contributing to the "Ghost Notes" thread. I have one of the JTV's (59) that has had some issues with the alternate tuning, so I guess I don't count as someone who has a "Perfectly Working" JTV. It is a strange anomaly, and I have thought a lot about whether I should choose option #1 or #2 also.
The problem with either one of those options for me is that I really LOVE this guitar. As just a regular 6 string electric, without the models & tunings, it really feels and plays better that most of the other off the shelf big brand guitars I have played (yes Fender and Gibson, I’m talking about you!). It is really resonant, sustains notes a long time, intonates really well. It's really solidly built, doesn't feel like a cheap knock off guitar. I am not having any problems with the neck and frets, no dead spots or fret buzz, the action is reasonably low, and I even like the neck contour. It's a little bigger than necks on some guitars I have owned or played, but feels really natural in my hands. I have had so much fun playing this guitar in the last couple of days that I think if someone’s going to take this guitar from me, they'll have to pry it out of my hands. It would really be difficult to take it back and hope to get another that plays as well.
Maybe I just got lucky and this is one of those instruments that you feel a connection with, and just sounds and feels right. I apologize, I’m gushing a little bit here but I really think this is a great instrument.
After re-reading what I just wrote, I don’t think I can choose option #1 or #2. The alternate tuning issue for me is a little sporadic anyway. It happens sometimes to a degree, on some combinations of models & tunings. I think I have no real choice but to hope that this is something that will be resolved through a software or firmware update. Maybe there’s some kind of hardware change that need to be done (updated circuit board or something), but I think I will keep this instrument, and hope that the issue can be resolved, or learn to live with it as is.