I have noticed that my JTV89 (original), particularly with the HD500x, has gotted very "honky" and piercing in the midrange, at around 1k. This hasn't always been the case. Also, the strat model has gotten more hollow and breathy sounding. I have to put an EQ pedal in front of the Pod and completely cut the 1k band to keep my ears from aching.
I have had the JTV89 for about 8 years now. Any chance this might be a side effect of a degrading piezo?