@Nivm: Ok, I didn't have much time to look at it last night, but I did find a few things while poking around. Looks like your raws are all messed up, with various things missing.
I tried to gen a new world, and got thousands of rejects even with no changes to the default settings for a Medium world. I had to allow all reject types just to get it to finish, so something is messed up in there. However, I did NOT see anything unusual in the population listings for that world.
I did walk around a little bit as an adventurer, and found a place full of Moghoppers. Vermin civilians apparently make things very strange. Since they didn't show up in the site population lists, I think the game is doing something odd after you show up.
My guess is that you've got some missing tokens and some duplicate tokens somewhere which is causing the problem. Any duplicate item/creature names (the actual name for the item, not the display name) will cause DF to do bizarre stuff like this. Basically you'll need to go though your raws and look for issues.
Here is the list of stuff I found in your error file after I tried to launch the game:
Missing Creature Definition: CHAOS_LORD
Unrecognized Entity Token: NAME
Unrecognized Entity Token: TILE
Unrecognized Entity Token: COLOR
Unrecognized Metal Token: CRYSTAL_BLOOD
Unrecognized Stone Token: MITHRIL
Unrecognized Stone Token: BLOOD_METAL
Unrecognized Stone Token: BLACKMETAL
Unrecognized Stone Token: MARBLE_BLACK
Unrecognized Stone Token: MARBLE_GREEN
Unrecognized Stone Token: MARBLE_BLUE
Unrecognized Stone Token: MARBLE_RED
CRYSTAL_FROST: Environment Spec Stone Not Found, Token - NIVOCITE
Unrecognized Metal Token: DRAGONSCALE_RAW
Unrecognized Metal Token: DRAGONSCALE_RAW
Unrecognized Metal Token: DRAGONSCALE_RAW
Unrecognized Metal Token: DRAGONSCALE_RAW
Unrecognized Metal Token: DRAGONSCALE_RAW
Duplicate Object: matgloss_plant COTTON
Duplicate Object: creature FOX_ARCTIC
Duplicate Object: creature BIRD_PHOENIX
Duplicate Object: creature ANT_GIANT
Duplicate Object: creature CHICKEN
Duplicate Object: creature PIG
Unrecognized Entity Token: NAME
Unrecognized Entity Token: TILE
Unrecognized Entity Token: COLOR
Unrecognized Metal Token: CRYSTAL_BLOOD
Unrecognized Stone Token: MITHRIL
Unrecognized Stone Token: BLOOD_METAL
Unrecognized Stone Token: BLACKMETAL
Unrecognized Stone Token: MARBLE_BLACK
Unrecognized Stone Token: MARBLE_GREEN
Unrecognized Stone Token: MARBLE_BLUE
Unrecognized Stone Token: MARBLE_RED
CRYSTAL_FROST: Environment Spec Stone Not Found, Token - NIVOCITE
Unrecognized Metal Token: DRAGONSCALE_RAW
Unrecognized Metal Token: DRAGONSCALE_RAW
Unrecognized Metal Token: DRAGONSCALE_RAW
Unrecognized Metal Token: DRAGONSCALE_RAW
Unrecognized Metal Token: DRAGONSCALE_RAW
Those duplicate tags would be the first I'd look at. You'll need to make sure you don't have any dups like that if you want DF to work properly.