I get the weirdest out-of-tune anomaly from all of the 12 string models on my JTV-89. I tune my guitar down a whole step (for singing purposes) and use the virtual capo for bringing it back up to standard pitch for some tunes. I would appreciate it if you can try this and report here if you get a clashing tone.
Here's what to do:
1) Tune your "D" string down to a "C" (no need to tune down other strings)
2) Pluck the second fret of the "D" string and immediately pluck the "D" string open
If you hear the "clashing tones", pluck other frets on the "D" string, then open for different pitch clashes
I typically use the second position Rick 12, but I notice this will all 12 string models
Much appreciate it.