Do you have Faction Cloaks, Marks or Bonds equipped?? This could be the issue, you rep will go to the Faction instead of Vanguard if you have one of these items equipped.
Edit: Yup, this is your issue, your rep is going to Dead Orbit.
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Thank you :) haha yeah i just read what the warlock bond said and it tells me its going to Dead Orbit haha thank you, wont be putting that thing on again :)