I'm confused....

Is the fine tuning knob too high or screwed all the way out?

If so, just unlock the strings at the nut, level all the fine tuners to where they are about half way screwed in, tune the guitar using the regular tuning pegs on the headstock, lock the strings back down at the nut, then fine tune with the fine tuners...

or

Is the entire Floyd Rose system sitting at too high of an angle, as in the back end is too high and not level with the guitar body?

If this is it, then the springs for the Floyd Rose need to be adjusted. Just take the back cover off of the guitar and tighten the claw (the thing that the springs are attached to). There will be 2 screws that connect the claw to the body of the guitar.....This can be an extremely aggravating adjustment as it has to be just right in order for the string tension and the spring tension to level out.....takes a lot of patience....have to adjust the springs, tune (which will take a while), adjust the springs, tune....and so on....until the Floyd sits parallel with the body of the guitar and is in tune.