I got this problem for quite a long time. My B string is always lower by 3 or 4 mm than the others. And i got this problem with my previous guitar which is of the Floyd Rose system too. Can anybody tell me how to solve tt problem?
One way is to check the height of the saddle which the b string is resting on. Usually there should be 2 tiny screws(using allen key) to adjust the height of the saddle and thus, the height of the string in relation to the fretboard
Another way is to check the slot on the nut for the b string, whether is it cut too low and as a result, the string is sitting too much in. This problem need more attention thou, from a guitar tech.