The problem is that at any time of the day, the cloud texture is this instead of what it's supposed to be:
http://yourimg.in/j/8s3kgj.jpg
Sorry if this is a common problem, it's been a long time since I've modded Morrowind.
EDIT: Through further testing, I'm sure of the following:
- It's not because of wrong Morrowind.ini weather settings
- It's not because of isplaced or alpha-less sky textures
- It's not because of one of my esps, as I ran a binary search, but I'll leave the load order here because you never know
- Sun disk is visible through the clouds
- The problem only sets in later in the game, the sky is fine in the beginning. It usually - but I always go there first - starts around Pelagiad or Balmora
Current load order:
Morrowind.esmTribunal.esmBloodmoon.esmabotWaterLife.esmMorrowind Patch v1.6.5-BETA.esmSG-MW-ecology-BM.esmGDR_MasterFile.esmTexture Fix - Bloodmoon 1.1.esmTexture Fix 1.8.esmMCA.esmBloodmoon Landscape Overhaul 1.0.esmMW_Children_1_0.esmBetter Heads.esmBetter Heads Tribunal addon.esmBetter Heads Bloodmoon addon.esmmaster_index.espLCV Schedule Markers.espNPC LCV Schedules 03.espLadyD_Reduced_Commentary.espLCV Wolverine Hall 01.espLight Sounds.espAtmosphericSoundEffects-3.0-Tribunal.espVivec_Voice_addon TRIBUNAL.espSound Enhancements.espLess Lore.espLGNPC_NoLore_v0_83.espLgnpc_SN.espHealers.espNPC LCV Locks.espDagoth Ur Voice Addon v1.0.espVivec Expansion 2.0.espLGNPC_GnaarMok_v1_10.espLGNPC_AldVelothi_v1_20.espCreatures.espDN_Umbra.espDN-GDRv1.espLGNPC_MaarGan_v1_20.espLGNPC_HlaOad_v1_32.espVality's Balmora Addon.espLGNPC_Aldruhn_v1_20.espWindows Glow.espKey Replacer Trib & BM.espLGNPC_Aldruhn_v1_20_suppl.espLGNPC_Pelagiad_v1_22.espLGNPC_TelMora_v1_20.espLGNPC_Khuul_v2_10.espLGNPC_VivecFQ_v2_10.espLGNPC_TelUvirith_v1_20.espLGNPC_SecretMasters_v1_30.espLGNPC_IndarysManor_v1_51.espLGNPC_VivecRedoran_v1_50.espabotWindowsGlow.espLess_Generic_Nerevarine.espLGNPC_PaxRedoran_v1_20.espLGNPC_SoulSicknessPatch_v1_00.espAreaEffectArrows.espNEDE v1.2.espRKCriminals TR&BM.espTravelingMerchants_v2.2.espDXM_masterindex_journalfix.espVOORHEES_AldIndoril2.espDagoth Gares_Voice_addon v1.1.espSpzInteriorDaylight.espTLM - AdjMod - Spuzzum's Interior Daylight.espLauranasReliefBelt.espClean Key Replacer MW Renamer.espDB_Attack_Mod3.espDivine_domina_part_1.espDivine_domina_part_2.espDivine_domina_part_3_Tribunal.espAlmalexia_Voicev1.espk_weather.espbarilzar_voice.espSirLuthor-Tools.espUnique Banners and Signs.espBetter Bodies.espDivine_domina_part_4.espVality's Bitter Coast Addon.espUniqueFinery_NoRobe.espUAR_ChodalaBoots.espWA_Signy_Signposts(!).ESPGCD v1.08 with Startscript, fixed [Galsiah].espWindows Glow - Raven Rock Eng.espEbonheart Fix.ESPMCA - Divine Domina Addon.ESPProtective Guards.espBetter Skulls.ESPMiscastModv3.0.espSeyda Neen Docks V7.0 Bloodmoon.espK_Potion_Upgrade_1.2.espKS_Julan_Ashlander Companion_1.3.espAuthentic Signs IT 1.1.espLeFemmArmor.espDivine_domina_part_5.espNymeria's Faster Walk.espRealistic Weather v2.0.espRKWerewolf.espadamantiumarmor.espk_in_tent.espBetterBooks_AlchFormfix.espWanderers of Solstheim.espBarabus Orcs.espSpect Sorcery pt 1.espVality's Ascadian Isles Addon.espRegional_Mana-BM.espRegional_Mana_Regen-MW+T+BM.espSlof's Pillow Book.espBetter Clothes_v1.1.espCR Ore Replacer 1.0.espAcheron's Camping Gear 2.espLGNPC_SecretMasters_MCA5.espFliggerty's Fleeing Fetchers.espLess_Generic_Bloodmoon.espBetterClothes_Patch.espBetterClothesForTB.espDN_1st_Person_Armor.espDN_Adamantium.espDN_IceBlade.espcorrectUV Ore Replacer 1.0.espWindows Glow - Tribunal Eng.espWindows Glow - Bloodmoon Eng.espLess_Generic_Tribunal.espTLM - Complete.espParticle Arrow Replacer.espAEA-Compatibility.espHelioS - Darker Weather.espDN_1st_Person_bodies.espVurt's Grazelands Trees.ESPLightTheWayScriptBM.espSiege at Firemoth.espNew Argonian Bodies (Slof Textures) - Clean.espNew Khajiit Bodies (Slof Textures) - Clean.espNo thieving start 1.0.espBarabus' fireplaces 2.espSol-Weather Tweak.espSG-MW-ecology-BM-plugin.espWaterfall v1.0.espentertainers.espIlluminated Windows.espASE Bloodmoon Expansion.espIlluminated Windows - Bloodmoon.espASE Tribunal Expansion.espSyc_HerbalismforPurists.espSyc_HerbalismforPurists_BM.espSyc_HerbalismforPurists_TB.espMournhold, The Great Bazaar.espClean Better Daedric.espUnique Jewelry and Accessories.espbones.espBetter Solsthiem Creatures.espA_flock_of_seagulls.espShieldfx.espabotWhereAreAllBirdsGoing.espWestly_Presents_Unique_Corprus_Stalkers.espEBQ_Artifact.espTLM - AdjMod - Siege At Firemoth.espWestly_Presents_Unique_Winged_Twilights.espMore Better Clothes.ESPBetterMusicSystem_1.8.espdej_plain_paper_fix.espUniqueFinery.espPiratelords Trade Enhancements.espTLM - Ambient Light + Fog Update.espPTE - BC Patch.espIceBradyHurdyRobeReplacerPLUS.espMashed Lists.espLibrarian with Jackets BM Trib.esp
I also have Morrowind Graphics Extender running.