I am having the same problem with my 59, sounds tinney when you enable the capo setting, not matter which guitar model you select, or the pickups you choose. Only thing that works is to put the capo setting in one of the alternative slots. Sucks I know.

I've seen several posts referring to this problem as well as my own pointing out that as of the latest POD HD500/Pro 2.02 (I think?)update, which was the same time as the JTV 1.81 update this situation has occurred.

What I've learned which yet again might have already been covered before my post here - is that the mags are coming through even though the player is not "asking" for them to sound simultaneously.

I got this result even when using a 1/4" standard cord into a conventional amp.  I thought by default it must be in the 1.81 update.  I rolled back to 1.71, then plugged back into the POD HD500 with it's latest update and got the same dual tone situation.

I went through all input options and found that the only time the dual sound stopped was when the input was set to "Variax Mags".  Which simply told me that there was some sort of communication error between the JTV and the POD HD with signals using Vax ch.1 and Vax ch.2.  What really had me stumped was the same dual sound happening plugged into a conventional amp.

What I managed to work out was if I switched the guitar on then off, then back on again - that cleared the problem most of the time.  Other times clearing the problem occurred when switching the alt tuning knob from one tuning to another then back to either MODEL because I had a Workbench created alt tuned patch or back to the Alt tuning knob position I wanted to work initially.

This was a very confusing glitch I reported the best I could as there are so many factors that cleared it up or perhaps were causing it.

If any are still having this dual sound problem - please try as I've suggested and if none of my successful attempts work for anyone reading, please PM me and I'll try to help you work through your own specific JTV tuning problem.  And this is after you've submitted an official trouble ticket to Line 6 tech Support.  They are going to be much much more aware of this situation than I, but I might be able to help in the meantime.

Take care,

Neal

PS - also for anyone not already aware reading this post - JTV 1.82 has been released and although it has been reported to have some problems during the upgrade phase - I can confirm that the 1.81 Workbench guilt acoustic alt tuning problems have been resolved perfectly.  Line 6 tech has also tried to accommodate those of us who prefer the sound of the 1.71 acoustic guitar models by putting a nearly dry/direct mic'd acoustic sound ("as if mic'd at the 12th fret" as stated in the update) by dialing the tone knob to "10".  This defeats nearly all ambience that was annoying some users with update 1.81.  You will notice where this feature starts and stops by slowly rolling the tone knob on these acoustic models from 10 to 0 and back.  There is a very audible difference that I would equate to the knob position "8" that changes from the original 1.81 ambient sound to this new drier sound for each of the five models in that bank.

I still feel that my suggestion of just adding back the original 1.71 acoustic models into Custom Bank 1 and just give us JTV players the choice to use, mix/match whichever of these acoustic models we like for the songs we use them for.  Line 6 has always been about giving guitarists freedom to choose from a wide variety, this would be a golden opportunity to bring a bit of those past days back without much difficulty in my limited understanding of how the JTV guts work.