To my knowledge the "favorite race" medal (in this case custom race) only counts games played from DL, not from DA or TA. Theoretically this is something that's on the list to be fixed as far as MV functionality goes, but for the moment if you want your custom race medal to show up you'll simply need to play and submit a game in DL as a custom race.
A Quote From Sole Soul
I think medals are cool so here is some info about how to get a custom race medal. Know this I am not sure if this is right or wrong but getting Karma do you ask for it or is it just given with out asking. I don't want to make anyone upset so I will ask you. If I ask for Karma for this info is it right or wrong of me? Just me let know so I can learn from it.
Hello 
@Cypher Thank you, I look at your scores and they blew me away 
My main character is:
Saint Mina
OK? May I ask how you do that? I click on your character and it took me there to your character info.
Order of the Bloody Rose of Orders Militant of Adepta Sororitas
Saint Mina of Opelia VII
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“We are at war with forces too terrible to comprehend. We cannot afford mercy for any of its victims too weak to take the correct course. Mercy destroys us; it weakens us and saps our resolve. Put aside all such thought. They are not worthy of Inquisitors in the service of Our Emperor. Praise his name for in our resolve we only reflect his purpose of will.”
Inquisitor Enoch,
Castigations on the Last Days
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