I'm actually one of these brown / "arab" new blacks you speak of incidentally (I'm from Algeria) and I haven't had this problem. But I do not have an accent and I've sort of "integrated" well within American culture. I can see where someone who is not so well-integrated and comes with an accent might see some trouble, but if they can code with quality and work in teams well, all that goes out the window.
In my experience once most middle eastern/arab people are "integrated", people see their appearance as vaguely mediterranean and don't really think twice about it.
I agree. I'd also add that I don't think that experience is the same as African-Americans. People do distinguish between middle-eastern/Mediterranean and African-American. At least in my experience.