I don't recognize that particular mod. My first guess would have been "Burial of a Tax Man", but I removed it from my mod load order and still got the warning.
Here's my mod load order list:
Spoiler _001_ Morrowind.esm
_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_ Raym's Absolutely Aleatory Accoutrements 3.0.esm
_011_ TR_Data.esm
_012_ TR_Mainland.esm
_013_ Less Lore.esp
_014_ shrinetext.esp
_015_ NX9_Guards_Complete.ESP
_016_ abotGondoliers.esp
_017_ Windows Glow.esp
_018_ LGNPC_NoLore.esp
_019_ Trainer Variety.ESP
_020_ Wyr Jeweler v1.01 c.120.esp
_021_ Balmora, Natar's House.esp
_022_ Raym's Vampire Rumors.esp
_023_ P.R.E. v4.0.esp
_024_ Unique Banners and Signs.esp
_025_ abotWhereAreAllBirdsGoing.esp
_026_ Windows Glow - Tribunal Eng.esp
_027_ Book Rotate - Tribunal v5.3.esp
_028_ TownSounds.esp
_029_ Windows Glow - Raven Rock Eng.esp
_030_ Turn Undead.esp
_031_ Book Rotate - Bloodmoon v5.3.esp
_032_ MDP - Dagon Fel.ESP
_033_ MDP - Gnaar Mok.ESP
_034_ abotWindowsGlow.esp
_035_ abotSiltStridersTR.esp
_036_ abotWindowsGlowTR.esp
_037_ abotTRWaterSound.esp
_038_ EmmasKhuul.esp
_039_ MDP - Ebonheart.ESP
_040_ Starfire lite.esp
_041_ MDP - Khuul.ESP
_042_ AragonMonk-v11.esp
_043_ NX9_Guard_LGTrib_patch.ESP
_044_ Book Jackets - Bloodmoon - BookRotate.esp
_045_ New Lord's Mail.ESP
_046_ Magical Missions.ESP
_047_ Donation to The Gods.ESP
_048_ Clean The Mortal Life of Vivec.esp
_049_ PB_IngredientWeight.esp
_050_ PB_SignpostsRetexturedTR.esp
_051_ Looking Good.esp
_052_ Better Bodies.esp
_053_ Meteor.esp
_054_ pge.esp
_055_ Fireflies.esp
_056_ EcoAdjDaedricDrops.esp
_057_ Healing.esp
_058_ BlightedAnimalsRetextured.esp
_059_ NPC Functionality.esp
_060_ abotRainSplash.esp
_061_ abotMoveOrTakeMyPlace.esp
_062_ JMS-shishi_door_fix.esp
_063_ Djangos Dialogue.ESP
_064_ Rincewind's_Luggage_1.2.esp
_065_ The Lucky Pick.esp
_066_ Rincewind's_Luggage_1.2_MWSE.esp
_067_ Caldera Mage Quarters.ESP
_068_ Vil's Indarys_1.2.esp
_069_ Clean_NON1.LoveintheTimeofDaedra.v1.02_Abot.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_ correctUV Ore Replacer 1.0.esp
_076_ Key Replacer Trib & BM.esp
_077_ Expanded Sounds 1.2.esp
_078_ Bloated Caves.esp
_079_ More Exquisite Clothes.esp
_080_ TriggerDBAttack.esp
_081_ SeriousWeather_BM.esp
_082_ Wanderers of Solstheim.esp
_083_ LGNPC_MaarGan.esp
_084_ Less_Generic_Bloodmoon.esp
_085_ Less_Generic_Nerevarine.esp
_086_ LGNPC_HlaOad.esp
_087_ LGNPC_Aldruhn_v1_20.esp
_088_ LGNPC_Aldruhn_suppl.esp
_089_ LGNPC_Pelagiad.esp
_090_ LGNPC_TelMora_v1_30.esp
_091_ Scrolls and SoulGems 1.1.esp
_092_ LGNPC_Khuul_v2_21.esp
_093_ LGNPC_VivecFQ.esp
_094_ abotGuardsTR.esp
_095_ LGNPC_TelUvirith_v1_20.esp
_096_ LGNPC_SecretMasters_v1_30.esp
_097_ LGNPC_IndarysManor_v1_51.esp
_098_ LGNPC_VivecRedoran.esp
_099_ LGNPC_PaxRedoran_v1_20.esp
_100_ abotBoatsTR.esp
_101_ abotRiverStridersTR.esp
_102_ Clerical Robes.esp
_103_ Less_Generic_Tribunal.esp
_104_ LGNPC_SoulSicknessPatch_v1_00.esp
_105_ ExclusiveFactions.esp
_106_ TheRedoran.esp
_107_ A_flock_of_seagulls.esp
_108_ Appropriate Greetings M - T - 1.5.2.esp
_109_ Chalk30-Base.esp
_110_ Master Trainers.esp
_111_ NX9_Guard_LGRedoran_Patch.ESP
_112_ AtmosphericSoundEffects-3.0-Tribunal.esp
_113_ Expanded Sounds.esp
_114_ Sound Enhancements.esp
_115_ XE Sky Variations.esp
_116_ Wilderness Sounds T & B.esp
_117_ Beds4Rent.esp
_118_ DXM_masterindex_journalfix.esp
_119_ abotWaterLifeTRaddon.esp
_120_ Raym's Simple Mana Regeneration.esp
_121_ SlaveEscort_v2_01.esp
_122_ Vivec Records Lore Friendly.esp
_123_ Book Jackets - Morrowind - BookRotate.esp
_124_ Illy's Solsteim Rumour Fix.esp
_125_ MDP - Maar Gan.ESP
_126_ MDP - Hla Oad.esp
_127_ Book Jackets - Tribunal - BookRotate.esp
_128_ MDP - Fort Buckmoth.ESP
_129_ New Randagulf's Fists.ESP
_130_ MDP - Sadrith Mora.ESP
_131_ Bound Armor Bugfix (Medium).esp
_132_ New Boots of Blinding Speed.ESP
_133_ EEC Expansion.ESP
_134_ Better Picks'n'Probs Diversity.ESP
_135_ Birds and Crickets.esp
_136_ PB_SmallerPotions.esp
_137_ PB_SignpostsRetextured.esp
_138_ abotShrines0GoldFix.esp
_139_ Clean__JH_Enhanced_Creeper.ESP
_140_ Tamriel Rebuilt Book Rotate.esp
_141_ Gedna 101.esp
_142_ Detailed_Imperial_forts.esp
_143_ AAA 3.0 Addon - Vanilla.ESP
_144_ Imperial Presence (No SN).esp
_145_ Graphic Herbalism.esp
_146_ Morningstars.ESP
_147_ dopeyNPC.esp
_148_ Flies.ESP
_149_ dopeyNPC-Lock.esp
_150_ Magic Diversity 1.0.ESP
_151_ dwemer_scrolls.ESP
_152_ Bal Isra Annex.ESP
_153_ Restored Stronghold Tileset.esp
_154_ Graphic Herbalism Extra (Correct UV).esp
_155_ ST_Alchemy_Base_1.1.esp
_156_ Dandera Selaro inventory fix.ESP
_157_ GH ES (1.2) Patch.ESP
_158_ GHE ES (1.2) Patch.ESP
_159_ dopeyNPC-Taverns.esp
_160_ dopeyNPC-Travel.esp
_161_ Graphic Herbalism TR.esp
_162_ Graphic Herbalism TR Extra.esp
_163_ Clean_md_Forge of Hilbongard.ESP
_164_ Mashed Lists.esp
I did add some pluginless replacer mods, but I thought they only write over existing files, not delete files. Wait a minute, you mention ships. I'll have to check the mod "flies" IIRC, it added sound effects of flies buzzing around and changed things re: corpses in sunken ships.
Edit: No, Flies isn't it either. Removing it from load list did not eliminate the warning. If it matters, afaict the warning appears at the time I start a new game after the intro starts but before Juib appears on screen in the prison ship or when I am resuming from a saved game