Pickup clearance affecting intonation

[r05c03]

I was recently working on intonating a G&L L-2000 that I recently acquired from another TB'er. I had a dificult time initially, even after trying several extra sets of strings. It seemed that the A and E strings were always flat at the 12th fret, even with the saddle depth adjustment screws (moving the saddle closer or farther from neck) adjusted maximally toward the neck (one more turn of the screw resulted in the saddle coming off of the screw. I solved the problem after I realized that the G&D string saddle depth screws were longer that the E&A. I Switcthed the screws from the G&D to the E&A which allowed me to move E&A saddles closer to the neck and achieve correct intonation at the 12th fret.

Then.....I adjusted my pick up height. When I rechecked inonation every single string was flat at the 12th fret. I freaked because I had spent quite awhile setting the bass up to my liking. When I lowered the Pickup, I found the strings were back at the proper inonation.

What gives, have others observed this. Is due to the magnetic pull of the pickups or what?

[Turnaround]

It's a common problem. When the pickups are too close to the strings, the magnetic pull causes intonation problems. I've run into that problem many times when setting up instruments.