Note that the OP's picture is a left handed guitar. It threw me off for a minute.
Is their a shim in the neck or in the floyd? Is the neck adjusted so that its flat and not bowing either way? Is the bridge parallel to the body?
Have you checked the intonation with a tuner?
If so, what is correct?
If so then don't worry about what it looks like.
If you have not checked it then check it...if you do check and it's correct then just play it, if it is not correct then set the intonation.
did you have brand new strings on when you did it?
My strat intonates like this:
e..|
B...|
G.|
D..|
A...|
E....|
Not sure why, but it's all intonated well and in tune, so whatever.
do you use a wound G?
Floyds have the bridge radius built into the saddle heights, and you shouldn't really need to shim the saddles to get the correct radius. But if you did, that might explain the shape you're seeing.