I have a fairly new JTV-89F that has a D string that is much quieter than the other strings. All the strings ring out clearly via the magnetic pickups, but the D string is considerably quieter than the rest through the piezo. The problem exists whether I'm connected via the Line 6 digital interface cable or via a regular 1/4 inch jack. I have verified the issue is also present on two different rigs. Firstly on an old Marshall VS65R amp with no pedals, and also on my new Line 6 DT50 with an HD500.
I have tried changing the strings and reseating them several times without any sucess. I have also upgraded to all the latest revisions of the Line 6 Monkey and all of the other associated software/firmware/drivers. I believe doing so does the equivalent of a factory reset on the guitar. I found a settings box in the workbench software that appears to show the individual string gain, and they were all set to 0 dB too. I can't imagine how the settings would have been anything other than the defaults, since I really haven't had a lot of time to dink around with this gear since I got it.
Any ideas what I can try to get my D string to normal?