A few ideas:
First of all, look at Rich Harris' excellent site with lots of good setup tips:
http://www.ibanezrules.com/tech/setup/index.htm
The
locking nut (TopLok) should be tight in 2 ways: the 3 screws on top that clamp the strings and the 2 Allen screws that hold the TopLok tight on the neck. The string clamps (pressure pads) should be snug enough, but not terribly tight. Don't wanna strip 'em.
The 2 Allen screws should be tight enough, but not enough to crack the wood. "Tight enough" is a feel thing. You'll know when they're tight enough.
Loosen the 3 pressure pad screws so that they're not clamping the strings at all. Ya don't havta remove them for this. Loosen the 2 Allen screws just a little bit. Put some pressure with fingers on the TopLok and press toward the bridge. Make sure the TopLok is snug against the neck and aligned/centered on the neck. Tighten the 2 Allens as you're applying pressure against the TopLok. This will make sure that the TopLok is in the right position and tight. If they're a little loose, the TopLok can wiggle around a bit and it'll affect tuning. (Thanks to Rich Harris for that tip!)
I always make sure that the strings are in the
bridge saddles in a straight line from the saddle grooves. If they're a little off-center and there happens to be any kind of burr in the saddle groove (even on the sides of the groove), that could make the third string jump a bit when you return the vibrato to neutral.
It's possible that there are flat spots or other anomalies in the bridge studs or the knife edges of the vibrato. Unfortunately, the best way to verify this is to take the vibrato off and inspect (a hassle).
It's natural that some of the strings will lift away from the saddle even a little when diving or pulling up.
Make sure that the bridge stud set screw is "tight enough". Whenever you adjust the height, loosen the set screw before you turn the bridge studs. Do the raising (shudder) or lowering (now you're talking!), and tighten the set screws again when done.
Make sure that the "saddle intonation screws" are tight enough and aren't moving around.
Some of these things are kinda unlikely but I thought I'd throw them in for good measure. There are a lot of things, some big and some small, that go into a good setup. Just about everything can be done by the user if we understand how this stuff works and inter-relates.
(You didn't ask for a book, did you?) No, I'm not a guru-I'm just an average user who's had/has 8 vibrato-equipped git-fiddles.
HTH
David