I have a JTV 69s that is experiencing similar symptoms. It will switch from 12 string to 6 string randomly or go from standard tuning to DropD..
Duplicated with ethernet & 1/4" cable plugged in to Helix or my standby POD XT Live. Not the best thing to happen if you are playing live..
The guitar went back to the dealer where I bought it (Long & McQuade) in Ottawa a few months ago for repairs. It seemed to fix the issue
but it has started up again. With the randomness of the occurrences I'm thinking this is most likely a hardware issue.
Do you recommend I log a support ticket?