I've just determined that this problem is not actually limited to custom races... it seems to be affecting all my saves since I installed patch 1.0X... it's really quite irratating.
iocaine
It's not the planets in my custom system, it's all class 0 planets, everywhere, except for custom planets like Jupiter. And no, I haven't had planets dissappear completely. Though I have verified that it happens when loading any save game, not just quick saves and not just at the beginning of the game. I didn't notice this happening when I first played a game as the Terrans, so I assume it is because I am playing a custom race.
Hm, it doesn't seem to be just quicksaves, but actually any save early in a new game. I'm not sure if this might be due in part to using a custom race, though I don't see how that could be connected.
I've been having the hardest time figuring out what is going on, but it seems that when I load from a quicksave, all class 0 planets revert the the same (I'm assuming default) texture, which looks quite ugly given the number of class 0 planets. I think it's loading the quicksave that does it... has this come up before?