I'm starting a new game and added six mods to my existing load order plus several pluginless replacers. The six mods were:
MD_Azurian Isles.esm
Clean_Modern Adventurer.esp
Wyr Jeweler v1.01 c.120.esp
Clean The Mortal Life of Vivec.esp
Broadsheets and Notice Boards.ESP
Clean_NON1.LoveintheTimeofDaedra.v1.02_Abot.esp
When I started the new game, the residents of Seyda Neen didn't show up but afaict NPCs from other mods did. I've used Wyr Jeweler off and on over years before without problems.
My initial testing - removing and adding each mod by itself seemed to suggest that Azurian Isles was at fault. But on the third try, the Seyda Neen NPCs populated the town. The bug (no Seyda Neen NPCs) has not repeated itself.
Here is the final load order, including the new ones, I'll be using for my new game
_002_ Tribunal.esm
_003_ Bloodmoon.esm
_004_ Morrowind Patch v1.6.4.esm
_005_ abotWaterLife.esm
_006_ Book Rotate.esm
_007_ Texture Fix 2.0.esm
_008_ Texture Fix - Bloodmoon 1.1.esm
_009_ Poorly Placed Object Fix 1.2.esm
_010_ RF - Furniture shop.esm
_011_ TR_Data.esm
_012_ TR_Mainland.esm
_013_ Raym's Absolutely Aleatory Accoutrements 3.0.esm
*** _014_ MD_Azurian Isles.esm
*** _015_ Clean_Modern Adventurer.esp
*** _016_ Wyr Jeweler v1.01 c.120.esp
_017_ Balmora, Natar's House.esp
_018_ Raym's Vampire Rumors.esp
_019_ Less Lore.esp
_020_ LGNPC_NoLore.esp
_021_ shrinetext.esp
_022_ NX9_Guards_Complete.ESP
_023_ abotGondoliers.esp
_024_ Windows Glow.esp
_025_ P.R.E. v4.0.esp
_026_ Unique Banners and Signs.esp
_027_ abotWhereAreAllBirdsGoing.esp
_028_ Windows Glow - Tribunal Eng.esp
_029_ Book Rotate - Tribunal v5.3.esp
_030_ TownSounds.esp
_031_ Windows Glow - Raven Rock Eng.esp
_032_ Turn Undead.esp
_033_ Book Rotate - Bloodmoon v5.3.esp
_034_ MDP - Dagon Fel.ESP
_035_ MDP - Gnaar Mok.ESP
_036_ abotWindowsGlow.esp
_037_ abotSiltStridersTR.esp
_038_ abotWindowsGlowTR.esp
_039_ abotTRWaterSound.esp
_040_ EmmasKhuul.esp
_041_ MDP - Ebonheart.ESP
_042_ Starfire lite.esp
_043_ MDP - Khuul.ESP
_044_ RF- Dongle's Delights.esp
_045_ AragonMonk-v11.esp
_046_ RF - Lady E's Extravaganza.esp
_047_ NX9_Guard_LGTrib_patch.ESP
_048_ Book Jackets - Bloodmoon - BookRotate.esp
_049_ New Lord's Mail.ESP
_050_ Magical Missions.ESP
_051_ Donation to The Gods.ESP
*** _052_ Clean The Mortal Life of Vivec.esp
_053_ PB_IngredientWeight.esp
_054_ PB_SignpostsRetexturedTR.esp
_055_ Looking Good.esp
_056_ Better Bodies.esp
_057_ Character Maker.esp
_058_ Meteor.esp
_059_ pge.esp
_060_ Fireflies.esp
_061_ EcoAdjDaedricDrops.esp
_062_ Healing.esp
_063_ Galsiahs Character Development.esp
_064_ BlightedAnimalsRetextured.esp
_065_ NPC Functionality.esp
_066_ abotRainSplash.esp
_067_ abotMoveOrTakeMyPlace.esp
_068_ JMS-shishi_door_fix.esp
_069_ Djangos Dialogue.ESP
_070_ LGNPC_SeydaNeen.esp
_071_ QTA_1.0.esp
_072_ LGNPC_GnaarMok_v1_20.esp
_073_ Galbedir Soulgems.esp
_074_ LGNPC_AldVelothi_v1_20.esp
_075_ Key Replacer Trib & BM.esp
_076_ Expanded Sounds 1.2.esp
_077_ More Exquisite Clothes.esp
_078_ Wanderers of Solstheim.esp
_079_ LGNPC_MaarGan.esp
_080_ LGNPC_HlaOad.esp
_081_ LGNPC_Aldruhn_v1_20.esp
_082_ LGNPC_Aldruhn_suppl.esp
_083_ LGNPC_Pelagiad.esp
_084_ LGNPC_TelMora_v1_30.esp
_085_ Scrolls and SoulGems 1.1.esp
_086_ LGNPC_Khuul_v2_21.esp
_087_ LGNPC_VivecFQ.esp
_088_ Bloated Caves.esp
_089_ abotGuardsTR.esp
_090_ Less_Generic_Bloodmoon.esp
_091_ Clerical Robes.esp
_092_ Less_Generic_Nerevarine.esp
_093_ LGNPC_TelUvirith_v1_20.esp
_094_ LGNPC_SecretMasters_v1_30.esp
_095_ LGNPC_IndarysManor_v1_51.esp
_096_ LGNPC_VivecRedoran.esp
_097_ LGNPC_PaxRedoran_v1_20.esp
_098_ abotBoatsTR.esp
_099_ abotRiverStridersTR.esp
_100_ LGNPC_SoulSicknessPatch_v1_00.esp
_101_ A_flock_of_seagulls.esp
_102_ Appropriate Greetings M - T - 1.5.2.esp
_103_ Chalk30-Base.esp
_104_ Master Trainers.esp
_105_ Less_Generic_Tribunal.esp
_106_ NX9_Guard_LGRedoran_Patch.ESP
_107_ AtmosphericSoundEffects-3.0-Tribunal.esp
_108_ Expanded Sounds.esp
_109_ Sound Enhancements.esp
_110_ TriggerDBAttack_v1_00.esp
_111_ Wilderness Sounds T & B.esp
_112_ Beds4Rent.esp
_113_ DXM_masterindex_journalfix.esp
_114_ TheRedoran_v1_00.esp
_115_ abotWaterLifeTRaddon.esp
_116_ SlaveEscort_v2_01.esp
_117_ Vivec Records Lore Friendly.esp
_118_ Book Jackets - Morrowind - BookRotate.esp
_119_ Illy's Solsteim Rumour Fix.esp
_120_ MDP - Maar Gan.ESP
_121_ MDP - Hla Oad.esp
_122_ SeriousWeather_BM_v1_00.esp
_123_ Book Jackets - Tribunal - BookRotate.esp
_124_ MDP - Fort Buckmoth.ESP
_125_ New Randagulf's Fists.ESP
_126_ MDP - Sadrith Mora.ESP
_127_ ExclusiveFactions_v1_01.esp
_128_ New Boots of Blinding Speed.ESP
_129_ Better Picks'n'Probs Diversity.ESP
_130_ Graphic Herbalism.esp
_131_ md_Forge of Hilbongard.ESP
_132_ Birds and Crickets.esp
_133_ PB_SmallerPotions.esp
_134_ PB_SignpostsRetextured.esp
_135_ abotShrines0GoldFix.esp
_136_ Bound Armor Bugfix (Heavy).esp
_137_ Clean__JH_Enhanced_Creeper.ESP
_138_ Tamriel Rebuilt Book Rotate.esp
_139_ Gedna 101.esp
_140_ Detailed_Imperial_forts.esp
_141_ RF - Bethesda Furniture.esp
_142_ Graphic Herbalism Extra.esp
_143_ AAA 3.0 Addon - Vanilla.ESP
_144_ Graphic Herbalism TR.ESP
_145_ Graphic Herbalism TR Extra.ESP
_146_ GHE ES (1.2) Patch.ESP
_147_ Imperial Presence (No SN).esp
_148_ ST_Alchemy_Base_1.1.esp
_149_ Dandera Selaro inventory fix.ESP
_150_ Morningstars.ESP
_151_ Magic Diversity 1.0.ESP
*** _152_ Broadsheets and Notice Boards.ESP
_153_ Vil's Indarys_1.2.esp
_154_ dopeyNPC-Taverns.esp
_155_ dopeyNPC-Travel.esp
_156_ dopeyNPC.esp
_157_ dopeyNPC-Lock.esp
*** _158_ Clean_NON1.LoveintheTimeofDaedra.v1.02_Abot.esp
_159_ Mashed Lists.esp
*** new from 5/5/15 total of six
It's the first time I've run into the residents of a town being a no-show at the start of a new game