The longer and deeper I get in, trying to do the perfect setup for my JTV-59 the harder I feel that the bridge is not placed well by the factory or specs.
If I try to setup the intonation well, I have to place the string-adjustment-sliders on the bridge (don't no the proper term for ist in English) back, at the very end, both on low E and A. There is no way to screw them more backwards so I am very glad, that this is the point, where intonation is okay but not perfect.
I am in contact with some other players of the JTV59 and they can confirm my guesses.
Besides there are some images of the 59er bridge in the web, witch indicates the same problem.
Of cause there are other images where the adjustment-sliders are shown the right way but I am pretty sure not everyone is even testing the intonation.
But here is also an older thread on this topic without any statement of L6
http://line6.com/support/topic/3630-jtv-59-intonation-problem-with-9s/?hl=jtv-59+intonation
String gauges I tried...
9-46
10-46
10-52
I even tried to proof the intonation using a capo and measuring the 13. fret.
Also the tiny screws at the bridge are adjusted as long as possible, without loosing the possibility to adjust the height of the bridge by covering this screws.
I would like to ask psarkissian if this is a known "issue" (you don't have to call it an issue as I am sure you are not allowed) so I can stop my search for the holy grail of intonation. Otherwise I like to ask for further advices getting the bridge adjusted the right way.