They're identical in both books except in Rogue Trader this talent allows the player to shoot semi/full auto bursts with half action, while in Only War there is no mention to that.
Which rule should I use?
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For the alternative viewpoint: The games in that series are, in many ways, the continuous evolution of what is essentially the same rule set. If Only War changed the effects of a Skill/Talent/Trait from those specified in one of the earlier games, then it seems likely that this is because the older version was found to be unbalanced or otherwise in need of revision.
Personally, if I were running a game using FFG's 40k rules, I would use the rules from Only War (or the Dark Heresy 2 Beta rules) as my baseline, then import or adapt the careers and any other necessary parts from the earlier games in the line.
If you're playing Rogue Trader, use the Rogue Trader version.
If you're playing Only War, use the Only War version.
They're two different games, and their mechanics have nothing to do with each other. The principle is pretty simple: use the rules for the game you're playing.