I may be missing the obvious here, so I hope I can get pointed in the right direction. When selecting a career, the game seems to suggest that you get all the skills, talents and gear in the grey box at the top of the page, but then some of those skills and talents are repeated in the first tier of advances.
The way I read it, if during character generation, you choose to buy one of the skills you already have in the grey box, then you get that skill at the second level (ie, at +10). Similarly, if you double up on a talent, you get the equivalent of Talented in that area.
Is that correct? One of my players has asked if the grey box is merely a suggested list, because he finds it odd that starting characters would get skill bonuses from the get-go, but it seems right to me, particularly taking into account that Rogue Trader characters are already at "level five" in terms of experience.
(Admittedly it doesn't help that the text is odd and ambiguous in places, such as listing the Missionary's Faith talent as a special ability when everyone else gets a special ability separate from their talents.)