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advanced empire settings don't effect the lost colony origin
Really? interesting thought it would, anyway I'm beginning to agree with OP as I have 3 human empires in my game 2 of which I created 1 has the lost colony origin and didn't start in sol (Cevant Empire) the other doesn't have the origin and is in sol. (Sol Republic) The game spawned another human empire that I didn't create that has lost colony as well (The commonwealth of man) So far I've been assuming that they both are from Sol Republic but now that I've thought about it I'm unsure if it is a bug or not.
 
It does seem like a bug as Commonwealth of man is a preset empire and the bio on them says lost colony from Earth which should in the Sol system so doesn't make sense that there is no other advanced humans anywhere in the galaxy of my game