I have also heard these "ghost notes" in alternate tunings, especially on the high e and b strings. I've also noticed that the effect is more pronounced when the high e string is tuned to a different pitch than the low e (in drop Db, for example). I believe that the cause is a sympathetic vibration of the low e string when the high e is plucked in an alternate tuning. I can hear the ghost note(s) until I mute the low e string after plucking the high e. If I mute the low e and a strings before I pluck the high e, then the ghost notes disappear, or are significantly lessened. This would explain why the effect is absent when the low e string is tuned to "e" (even in an altered tuning), since the sympathetic vibration would be at the same pitch as the one through the piezo. Any thoughts on this?