I had exactly this happening too, JTV-69 and HD-500 and I wanted a capo at the third fret so I set the Patch to alter the JTV tuning to +3 on all strings.  When I first did this it worked fine, and then a week later and with no idea what happened I was getting both standard and capo tunings at the same time.  It was not HD input settings and it was not hearing the strings, you got both tunings whether using VDI or 1/4 cable so it was the JTV that was corrupted, but what caused it? Don't know.

With an audition in 3 days time that required the third fret capo my recovery method was to reflash both JTV and HD500 and then recreate the relatively simple patches involved.

I wouldn't call this a fix because it isn't - something in the combined systems caused the JTV to output both sounds and I have no idea what, so it could happen again at any time.

I only connected the computer for long enough to apply the firmware and then did everything else locally on the HD and since then I have been very strict about disconnecting the two before powering off and only plugging the JTV back in after the HD-500 is completely booted and so far it hasn't happened again.  But that might just be luck.

The impact of this is catastrophic in terms of sounds and the process for recovering from it is rather long winded - if it happens again I will do my best to work out what might have triggered it, but I now carry a capo just in case it happens at rehearsal or before a gig.  If it happens in the middle of a gig it will be rather embarrasing...

I just wonder if it is related to the fault as yet not fixed where coming out of the HD tuner causes the JTV tuning to reset to standard?