When I made a character for Dark Heresy (many moons ago) I believe that the starting skills listed with the career path were all considered 'trained'. This idea was reinforced by the fact that they weren't listed in the Rank 1 advances. So, when I started making my new character for Rogue Trader, I expected the same thing. But, most of the starting skills are also listed in the advances for Rank 1. I'm not sure why they would be listed there if the character gets them for free, unless they're there for characters coming in from DH.
Anyway, I couldn't find anything that explicitly stated that "new characters are considered trained in their starting skills".