Old tip, and you probably have read it, but ...
Detune the guitar and bring it slowly back into tune again ... Seriously. And *slowly*.
Bring it down until you feel comfortable with the tension (this could be some notes down). Make sure it's "about" in tune at that position, i.e. as if you were playing with EbAbDb ... or even lower tuning.
Then work your way up until it's in tune, work on all strings at the same time. Turn all the tuners about half a turn, repeat, repeat, repeat until you're done. Just keep an eye on your tuner so one string doesn't rocket, they should all follow about the same pace.
If one string goes sharp while you're tuning, don't try to lower it, some other string(s) has/-ve gone flat - raise them instead and the sharp string will lower. Otherwise every other string will go sharp.
Ideally, all strings should get in tune at the same time.
Check the tremolo angle at this point, if it's not correct - adjust and retune.
This tip comes originally from http://www.ibanezrules.com/tech.htm
, "Tuning The Floating Tremolo" (and Ibanez instructions) and it can do wonders
It takes some time but it's well worth it. Read that and do exactly as it's written, don't try to hurry.