Intonation Troubles with 52RI and Peterson VSII

I have a 52RI Tele with Glendale compensated saddles(which I love) but I CANNOT get the 5th and 6th string to intonate correctly, even when using my Peterson VSII tuner! The A string is close...but E is almost always out. I also have installed on this guitar Lindy Fralin Blues Specials. When setting intonation (using brand new Ernie Ball Super Slinkys(9-42)) I put the pickup selector in the middle position. After getting things about right I can switch the selector to the bridge position and, almost always, everything(especially the E and A strings) is sharp. How close should I have this pickups? Right now I can't give you a measurement on how close they are, but they're NOT that close to the strings. I love these pickups too.

Where should I start on this thing...? What could be happening?

Thanks for the help.

Intonation could be off for a bunch of reasons. One easy thing you should check is that the saddles aren't shifting left or right. That turned out to be the problem when I was setting the intonation on my guitar with compensated saddles.

You could also try to check and see if your bridge pickup is too high. From what you're telling us, when you switch to the bridge position, the E and A are always sharp. If the pickups are too high, the magnetic pull from the pickups will pull the strings sharp. Also, 9-42 strings are more of a P.I.T.A. to intonate than some other guages.

I see that you already mentioned the pickups. DUH!! What's the action set to? How much relief do you have in the neck? Is the nut cut properly? Are the frets leveled properly? These are things that need to be considered BEFORE intontating a guitar. Intonation is the last step that needs to be done. If everything has been done and you are still off just remember that even though the saddles are compensated, you still are working with three saddles. What adjustments you make to one string will affect the other.

You could also try to check and see if your bridge pickup is too high. From what you're telling us, when you switch to the bridge position, the E and A are always sharp. If the pickups are too high, the magnetic pull from the pickups will pull the strings sharp. Also, 9-42 strings are more of a P.I.T.A. to intonate than some other guages.

Thats it, I bet. Lower that pickup a bit and see what happens.