On maps in which there are very few stars with habitable planets, for example, on a tiny map with habitable planets, planets, and stars set to "Rare", when I try to play using a custom race, the home star that I get is called Custom Star, and my home planet does not have a Civilization Capital, but rather has an Initial Colony. This kills my economy because now my home planet only produces 5 mt/wk of food rather than the usual 10. I also don't get a nearby low-class planet like I usually do. I can reproduce this fairly predictably.
This issue does not occur when I use a built-in race.
I think what is happening is that there are not enough habitable planets to go around for all of the races in the galaxy, so the game generates a star that has one but goofs when it's generating the home planet, but I'm not on the programming team, so this is just a wild guess. As a programmer myself, that's at least where I would look first.