I was reading throught the book of judgement and it states that all arbites are recruited from the schola progenium? how does that work when in character creation you can choose any background for the arbites, am i missing something?

The same paradox is presented in the Ascension book. Ascension "fluff text" indicates that Storm Troopers are drawn from Schola students, though there are rare examples of older candidates training alongside the younger recruits, but the Assassin and the Guardsman are the only characters that can choose the Storm Trooper Ascended Career. What's to say a Feral Worlder that rises through the Ranks of the Imperial Guard can't train with a bunch of kids and get his Storm Trooper jump wings? Nothing. Fluff-wise he is older and past his prime physical health and has to work harder to cut the mustard, but as far as character creation mechanics are concerned it's just a matter of earning and spending XP.

Simply put: fluff text puts things into perspective and gives recruitment for the Adeptus Arbites a context to understand the greater picture within the Imperium. An Arbites Character can certainly come from any world and any background, including the Tainted Blood of Malfi. An Arbitrator character could even have been recruited from a Blighted Schola! It's also important to remember that Arbitrators never serve their service with the Adeptus Arbites on their home world.