Ok dude, I think I know what the problem is.

You have what is known as a floating trem. This means that the bridge is kept in place by two forces. One is the force exerted by the springs in the cavity in the back of the guitar. The second balancing force is that exerted by your strings.

Consequently when you adjust the tension of one string (like tuning it) the other strings compensate and their relative tension (dictating their pitch) also changes.

So, undo any locking nuts and move any fine tuners to their middle position extinguish any smoking material and lock your seats in an upright position.

Then, tune your bottom E then your A then your D etc until your top E is at pitch. Then go back and do your bottom E again. Then re- tune to A, D, G etc. Once your top E is re- tuned (to pitch) start the process again. You will notice that the bottom E string is less out of tune than it was before. Now, repeat this process until, when you tune your top E, your bottom E is still in tune.

All floating trems have this problem and it is a huge pane in the behind.