Last fall I picked up a very clean G&L JB Tribute in a good pawn shop. I installed Labella Flexible Flats on it, and I've never been able to intonate it correctly.
I checked witness points, winding, string installation, and I still had trouble getting the bridge saddles extended far enough to get the pitch at the 12th fret to match the open string. The stock saddle adjustment screws wouldn't move the saddles out far enough to intonate.
I finally bought matching stainless steel screws 20 MM longer than the stock screws, and ground the diameter of the pan heads down enough to fit the bridge recess where they insert.
The photo below is what I have now; three of the four strings are intonated correctly, but the D is still a touch flat at the 12th fret. I've had to extend the saddles to the very front of the bridge or even slightly beyond to intonate the strings.
I've never had a problem like this before. I'm starting to suspect that the bridge is installed about 3/4 - 1/2" too far from the neck, and the result is that the saddles need to be extremely extended to intonate.
Thoughts? Suggestions?