So I've been following this off and on for some time since I have a JTV-89 with the hard tail bridge. My low E string sounds "plinky" as one poster eloquently described. I filed a ticket with Line 6 and received this response:
We have been involved in this thread online for a while. There is no issue with your guitar.
The short answer is piezos sound different than mag pickups because the string rests across the pickup element.
The larger the string the more pressure.
More pressure = frequency build up.
If you are using a guitar model or amp that already has a lot of build up in the high-mids you are going to hear a "plink" especially at high gain levels. This can be EQ'ed out and is not anything outside of the normal operation of the guitar.
You can hear this same sound on a lot of acoustic/electric guitars that use piezo systems. It's just not as apparent because you are not using high gain effects.
At first I thought, no way, it sounds to me like a cocked wah on the low E string, maybe bad filtering either in hardware or software. So the first thing I did to prove this wrong was take an A string I had laying around (0.36" diameter) and put it in place of my low E. I tuned it first to A, then to E, and sure enough in both tunings the plink disappeared. So it must be harmonics or vibrations on the fat E string.
Next, I took a piece of felt I had and cut a very small strip and placed it over the piezo below the string. Viola, problem is about 90% gone, definitely subtle enough that no one would notice unless I told them. In the following recordings, the first section is the magnetic pickups, then the piezos in standard tuning, then the piezos in 1 Down tuning. So here is a recording before the felt strip:
And the recording after putting in the felt strip:
And here are some photos showing the felt and what it looks like installed:
The felt must be acting as a damper to dampen out the ringing and excessive vibration of the fatter E string.
My next task is to dampen the strings at the nut with some Velcro or something. You can definitely hear the ringing when using the piezos.
I hope this helps some of you guys. It sounds way better to me and just saved me from selling this guitar. I wanted the Dream Rig, and the crappy sound of the low E string when chugging was definitely not part of that Dream!