This feels like a legit problem, but I'm not sure.
[CREATURE:BONGO_BSTORM]
[DESCRIPTION: A large, heavy-bodied antelope with large, curving horns and striking white markings.]
[NAME:bongo:bongos:bongo]
[CASTE_NAME:bongo:bongos:bongo]
[CHILD:1][GENERAL_CHILD_NAME:bongo calf:bongo calves]
[CREATURE_TILE:'B'][COLOR:7:0:1][POPULATION_NUMBER:15:30]
[PETVALUE:500]
[PET_EXOTIC]
[STANDARD_GRAZER]
[VISION_ARC:50:310]
[PREFSTRING:attractive markings]
[PREFSTRING:graceful horns]
[GRASSTRAMPLE:0]
[LARGE_ROAMING][MUNDANE]
[POPULATION_NUMBER:15:30]
[CLUSTER_NUMBER:3:7]
[BIOME:SHRUBLAND_TROPICAL]
[BIOME:FOREST_TROPICAL_MOIST_BROADLEAF]
[BENIGN][MEANDERER][NATURAL]
[BODY:QUADRUPED_NECK_HOOF:TAIL:2EYES:2EARS:NOSE:2LUNGS:HEART:GUTS:ORGANS:THROAT:NECK:SPINE:BRAIN:SKULL:MOUTH:TONGUE:GENERIC_TEETH:RIBCAGE:2HEAD_HORN]
[BODY_DETAIL_PLAN:STANDARD_MATERIALS]
[USE_MATERIAL_TEMPLATE:HOOF:HOOF_TEMPLATE]
[USE_MATERIAL_TEMPLATE:HORN:HORN_TEMPLATE]
[BODY_DETAIL_PLAN:STANDARD_TISSUES]
[USE_TISSUE_TEMPLATE:HOOF:HOOF_TEMPLATE]
[USE_TISSUE_TEMPLATE:HORN:HORN_TEMPLATE]
[BODY_DETAIL_PLAN:VERTEBRATE_TISSUE_LAYERS:SKIN:FAT:MUSCLE:BONE:CARTILAGE]
[BODY_DETAIL_PLAN:BODY_HAIR_TISSUE_LAYERS:HAIR]
[SELECT_TISSUE_LAYER:HEART:BY_CATEGORY:HEART]
[PLUS_TISSUE_LAYER:SKIN:BY_CATEGORY:THROAT]
[TL_MAJOR_ARTERIES]
[BODY_DETAIL_PLAN:STANDARD_HEAD_POSITIONS]
[BODY_DETAIL_PLAN:HUMANOID_RIBCAGE_POSITIONS]
[USE_MATERIAL_TEMPLATE:SINEW:SINEW_TEMPLATE]
[TENDONS:LOCAL_CREATURE_MAT:SINEW:200]
[LIGAMENTS:LOCAL_CREATURE_MAT:SINEW:200]
[HAS_NERVES]
[USE_MATERIAL_TEMPLATE:BLOOD:BLOOD_TEMPLATE]
[BLOOD:LOCAL_CREATURE_MAT:BLOOD:LIQUID]
[CREATURE_CLASS:GENERAL_POISON]
[GETS_WOUND_INFECTIONS]
[GETS_INFECTIONS_FROM_ROT]
[USE_MATERIAL_TEMPLATE:PUS:PUS_TEMPLATE]
[PUS:LOCAL_CREATURE_MAT:PUS:LIQUID]
[BODY_SIZE:0:0:19000]
[BODY_SIZE:1:0:100000]
[BODY_SIZE:2:0:300000]
[BODY_APPEARANCE_MODIFIER:LENGTH:90:95:98:100:102:105:110]
[BODY_APPEARANCE_MODIFIER:HEIGHT:90:95:98:100:102:105:110]
[BODY_APPEARANCE_MODIFIER:BROADNESS:90:95:98:100:102:105:110]
[MAXAGE:10:15]
[ATTACK:KICK:BODYPART:BY_CATEGORY:HOOF_FRONT]
[ATTACK_SKILL:STANCE_STRIKE]
[ATTACK_VERB:kick:kicks]
[ATTACK_CONTACT_PERC:100]
[ATTACK_PREPARE_AND_RECOVER:4:4]
[ATTACK_PRIORITY:MAIN]
[ATTACK_FLAG_WITH]
[ATTACK_FLAG_BAD_MULTIATTACK]
[ATTACK:KICK:BODYPART:BY_CATEGORY:HOOF_REAR]
[ATTACK_SKILL:STANCE_STRIKE]
[ATTACK_VERB:kick:kicks]
[ATTACK_CONTACT_PERC:100]
[ATTACK_PREPARE_AND_RECOVER:4:4]
[ATTACK_PRIORITY:MAIN]
[ATTACK_FLAG_WITH]
[ATTACK_FLAG_BAD_MULTIATTACK]
[ATTACK:BITE:CHILD_BODYPART_GROUP:BY_CATEGORY:HEAD:BY_CATEGORY:TOOTH]
[ATTACK_SKILL:BITE]
[ATTACK_VERB:bite:bites]
[ATTACK_CONTACT_PERC:100]
[ATTACK_PENETRATION_PERC:100]
[ATTACK_FLAG_EDGE]
[ATTACK_PREPARE_AND_RECOVER:3:3]
[ATTACK_PRIORITY:SECOND]
[ATTACK_FLAG_CANLATCH]
[ATTACK:HGORE:BODYPART:BY_CATEGORY:HORN]
[ATTACK_SKILL:BITE]
[ATTACK_VERB:gore:gores]
[ATTACK_CONTACT_PERC:100]
[ATTACK_PREPARE_AND_RECOVER:3:3]
[ATTACK_FLAG_WITH]
[ATTACK_PRIORITY:MAIN]
[CREPUSCULAR]
[HOMEOTHERM:10067]
[APPLY_CREATURE_VARIATION:STANDARD_QUADRUPED_GAITS:900:438:292:146:1900:2900] 60 kph
[APPLY_CREATURE_VARIATION:STANDARD_SWIMMING_GAITS:9000:8900:8825:8775:9500:9900] 1 kph, NO DATA
[APPLY_CREATURE_VARIATION:STANDARD_CRAWLING_GAITS:9000:8900:8825:8775:9500:9900] 1 kph, NO DATA
[SWIMS_INNATE]
[MUNDANE]
[CASTE:FEMALE]
[FEMALE]
[MULTIPLE_LITTER_RARE]
[SET_TL_GROUP:BY_CATEGORY:ALL:HAIR]
[TL_COLOR_MODIFIER:CINNAMON:1]
[TLCM_NOUN:hair:SINGULAR]
[CASTE:MALE]
[MALE]
[SET_BP_GROUP:BY_TYPE:LOWERBODY][BP_ADD_TYPE:GELDABLE]
[SET_TL_GROUP:BY_CATEGORY:ALL:HAIR]
[TL_COLOR_MODIFIER:DARK_BROWN:1]
[TLCM_NOUN:hair:SINGULAR]
[SELECT_CASTE:ALL]
[SET_TL_GROUP:BY_CATEGORY:ALL:SKIN]
[TL_COLOR_MODIFIER:BROWN:1:BURNT_UMBER:1:CINNAMON:1:COPPER:1:DARK_BROWN:1:DARK_PEACH:1:DARK_TAN:1:ECRU:1:PALE_BROWN:1:PALE_CHESTNUT:1:PALE_PINK:1:PEACH:1:PINK:1:RAW_UMBER:1:SEPIA:1:TAN:1:TAUPE_PALE:1:TAUPE_SANDY:1]
[TLCM_NOUN:skin:SINGULAR]
[SET_TL_GROUP:BY_CATEGORY:EYE:EYE]
[TL_COLOR_MODIFIER:BLACK:1]
[TLCM_NOUN:eyes:PLURAL]
And it seems to mess with the spawning of creatures on the embark. The creatures gen just fine, but the regional list of creatures is greatly impoverished - about half what it ought to be. And this time, there are no shelledfish on embark at all, and after waiting a bit they don't spawn either. Deleting the creature from the raws hasn't fixed it either, and this definitely wasn't happening before, since I've been checking region pops upon embark as a matter of course. Sometimes I'll get pond turtles, but in much-reduced numbers. Meanwhile, all the plants are listed as "innumerable" within the region, which is just untrue.
...Huh. Copying and pasting in "healthy" raws from an existing world didn't fix it.
EDIT: Removing the modded creatures didn't help, removing some other mods didn't help, removing the modded raw file didn't help. I took all the raws from an okay region and pasted them in...nothing. There's no way this can be "normal" like the last time, because it interferes directly with gameplay - since oysters and mussels are immobile, they will never "move in" into the map. They gen just fine, but they never, ever appear on the map. This has persisted across 5-10 worldgens, so it's not just an isolated incident. Errorlog, as usual, is completely useless. And I just figured out the other problem too...
I removed the thing that could have caused it, plus other things, but no dice. I just don't understand what went wrong.
EDIT: EDIT: No luck with even a fresh install. The only thing I can think of is some "unable to save" thing in my text editor (sublime text 2) or backup saves from it, but I don't know how to fix those. This is shaping up to be an absolute nightmare, just like last time.
I tried two, three fresh reinstalls, but the problem persisted. I'd write it off as a normal variation but for the fact that this complete absence of shellfish creatures from all embark points (although present in the world apparently) is a literal death sentence to any dwarf who likes shells. I've every possible offending thing but it still persists. Yet I know this isn't supposed to happen. Shellfish are either there on embark or not at all, and in over a dozen genned worlds, it's been "not at all".
MORE EDITS: So apparently I let some dwarves clean fish and the mussels came out of thin air? And it appears "innumberable" is the number of trees on my "healthy" files as well? Well, damn. I...really do not feel smart right now. And I think I know what was happening: I got local region pops mixed up with worldwide region pops. So disregard this entire post, I suck idiomatic cocks.