This has happened to me a few times (NXS1 players).
Unfortunately, there's nothing you can do.
You can't get an exchange as it's not a "manufacturing fault" and if you did, chances of you getting a player the same as the other one is 50/50.
I remember when I bought my NXS2 players and praying that the jog lights lit up the same brightness when I switched them on, which to my joy did!
I don't know the reasoning behind the different brightnesses.
I'd say the parts used in one player are from a different manufacture than the other CDJ.