It sounds like the default species used for empty colonies has managed to get set to a null/erroneous value instead of the main species of your empire. It isn't happening when you drop off colonists because the faulty species of the initially empty colony gets overwritten by the species of the colonists placed there.
Did you create the game by initially creating the sol system and then deleting it after setting up your new homeworld? If so did you make sure a capital was set once sol had been deleted? Did the problem start from the first colony/CMC that was founded or did it appear later?
Has the game been modified using the dev password? if not you may want to post it up over in the bugs section of the aurora forum.
It may be just a glitch in this particular game but if you are going to scrap it I'd suggest restoring from your backup of the originally installed database.
That's essentially the conclusion I've reached as well.
1. I used the SM Race start, so I believe not.
2. Yep, the world I started on is correctly identified as my capitol.
3. It began with the first CMC and has reoccured in every non-colonist founded colony thusfar.
4. No dev mode modification at all.
As of the moment, the /0 errors have stopped for the only currently existing CMC, though I'm not sure why, as all the other symptoms of the problem persist. I'm not too deep into this game (less than a decade), so I think I'll just start a new game and make sure it is confined to this particular save. I'm tempted to identify it as being related to the fact that it isn't a Sol start, as that is the only "new" thing about this game as compared to previous ones. Meh, nichevo. Maybe I'll bump the difficulty modifier up to 1000% and the NPR gen rate to 75% or so this time around; Swarm and Precursors alone get boring after a while.