Lately I've been getting a random fps issue. I go into an interior and then come out, only to be hit by an fps hit which puts me in slide-show mode below 5 fps. If I reload my game and then leave the same interior, I no longer have the issue and can continue on with my game. Once when this happened I was able to find the culprit, which was an NPC in Gnisis, who when I killed and disposed of the body, the fps hit went away immediately. Other than that one NPC (whom I'm afraid I forgot to write down the name) I've never been able to find out the cause of the fps hit, including using the "disable" console command. This has happened 4 or 5 times in different locations, the latest being in Balmora.

Any ideas? My mod list for what its worth:

Masters for Xi60000.ess:001  Morrowind.esm002  Tribunal.esm003  Bloodmoon.esm004  Morrowind Patch v1.6.4.esm005  Texture Fix 1.8.esm006  Texture Fix - Bloodmoon 1.1.esm007  Morrowind Advanced.esm008  abotWaterLife.esm009  Book Rotate.esm010  The Undead.esm011  GDR_MasterFile.esm012  Havish.esm013  BT_Whitewolf_2_0.esm014  Hilgya the Seamstress.esm015  Galsiahs Character Development.esp016  GCD StartScript for Trib or Bloodmoon.esp017  GCD better balanced birthsigns.esp018  GCD Over 60 level speedup.esp019  GCD Restore Potions Fix.esp020  GCD settings hard.esp021  GCD_107x_to_108_patch.esp022  KS_Julan_Ashlander Companion_1.3.esp  (Version 1.3)023  ImprovedTeleportation2.0.esp024  abotGuars.esp  (Version 1.15)025  AreaEffectArrows.esp026  master_index.esp027  LeFemmArmor.esp028  adamantiumarmor.esp029  EBQ_Artifact.esp030  Siege at Firemoth.esp031  LadyD_Reduced_Commentary.esp032  Quieter_UI_Sounds.esp033  Sleepers-fix.esp  (Version 1.1)034  MinerPickUseGOTY.esp035  MuckShovelUse.esp036  ElementalShield_Fix.esp037  AscendedSleeperSFX.esp038  Steel Broadsword Fix BM.esp039  HospitalityPapers.esp040  GnisisEggminePass.esp041  Faction Hellos.esp042  Book Rotate - Tribunal v5.3.esp043  Book Rotate - Bloodmoon v5.3.esp044  PotionSorter.esp045  DremoraLootEnhancementMWA.esp046  EBJ_spell_organizer.esp047  NoShieldEffect.esp048  The Holiday Mod.esp049  BT_Whitewolf_2_0NOMaddon.esp050  Havish - Scimitar Update + GCD (no MWE).esp051  havish13_nom_patch.esp052  Havish Mini Patch.esp053  The Sable Dragon.esp054  correctUV Ore Replacer 1.0.esp055  Clean chapelsv2.esp056  Less Lore.esp  (Version -01)057  Better Bodies.esp058  New Argonian Bodies - Mature.esp059  New Khajiit Bodies - Mature.esp060  Balance - NPC Spellcasting.esp061  Balance - game settings.esp062  Gameplay - Faction.esp063  Gameplay - Dialogue.esp064  Balance - Magic Effects.esp065  Balance - spells.esp066  Balance - Character.esp067  Balance - items.esp068  Chargen_Revamped_v2_1.esp069  Improved Skilled Magicka.esp070  Homes To Let.esp071  Rain's Hand Hall.esp072  Larger Indarys 1.1.esp073  Larger Indarys Manor.esp074  Abu Manor v.2.esp075  Hair_pack.esp076  Hair_Pack_I.esp077  Hair_Pack_II.esp078  Hair_Pack_III_Tiaras.esp079  Hair_Pack_IV_Lora_Redone.esp080  Rhedds_WE_F_expanded.esp081  UQFsMasterFacePack.esp082  Westly's Master Headpack X.esp083  House of Mannequins v1.0.esp  (Version 1.0)084  axels_piercings.esp085  Hilgya the Seamstress Expansion 1.esp086  Scissors & Thimbles Merge.esp087  Jeremy's Knights of Tamriel & Valshea.esp088  Netch Adamantium Armor II.esp089  sm_netchadamantium_Weapons.esp090  Better Clothes_v1.1.esp091  BetterClothesForTB.esp092  Book Jackets - Morrowind - BookRotate.esp093  Book Jackets - Tribunal - BookRotate.esp094  Book Jackets - Bloodmoon - BookRotate.esp095  Divine_domina_part_1.esp096  Divine_domina_part_2.esp097  Divine_domina_part_3_Tribunal.esp098  Divine_domina_part_4.esp099  Divine_domina_part_5.esp100  Dagger of Symmachus.esp101  Textured_Signs_Neutral.esp102  moons_soulgems.esp103  Better Skulls.ESP104  Lantern replacer By Leeloo.esp105  Windows Glow.esp106  MW_Adv_Required.esp107  Haunted Tombs v1.06.esp  (Version 1.06)108  farrp_WeaponCompilationMod_V2.esp109  MoreGems.esp110  Pearls Enhanced - Colored Pearls Add-on.ESP111  sg1_alchemy_book.esp112  Expanded Sounds.esp113  Hold it replacer.esp114  Hold it - NOM addon.esp115  NX9_Guards_Complete.ESP116  Ald Redaynia Extended.esp117  Guarded GhostGate.esp118  Clean Atmospheric Balmora.ESP119  MDP - Maar Gan - 1.0.ESP120  MDP - Khuul - 1.0.ESP121  MDP - Ebonheart.ESP122  MDP - Dagon Fel.ESP123  New Gnaar Mok.ESP124  Clean New Seyda Neen 1.5.esp125  New Gnisis.ESP126  Animated Morrowind 1.0.esp127  LGNPC_NoLore_v0_83.esp  (Version 0.83)128  Lgnpc_SN.esp  (Version 0.31)129  LGNPC_GnaarMok_v1_10.esp  (Version 1.10)130  LGNPC_AldVelothi_v1_20.esp  (Version 1.20)131  Less_Generic_Nerevarine.esp132  Less_Generic_Tribunal.esp133  LGNPC_MaarGan_v1_20.esp  (Version 1.20)134  LGNPC_HlaOad_v1_32.esp  (Version 1.32)135  LGNPC_Aldruhn_v1_20.esp  (Version 1.20)136  LGNPC_Aldruhn_v1_20_suppl.esp137  LGNPC_Pelagiad_v1_22.esp  (Version 1.22)138  LGNPC_TelMora_v1_20.esp  (Version 1.20)139  LGNPC_Khuul_v2_10.esp  (Version 2.10)140  LGNPC_VivecFQ_v2_10.esp  (Version 2.10)141  LGNPC_TelUvirith_v1_20.esp  (Version 1.20)142  LGNPC_SecretMasters_v1_30.esp  (Version 1.30)143  LGNPC_IndarysManor_v1_51.esp  (Version 1.51)144  LGNPC_VivecRedoran_v1_50.esp  (Version 1.50)145  Less_Generic_Bloodmoon.esp  (Version 1.1)146  LGNPC_PaxRedoran_v1_20.esp  (Version 1.20)147  LGNPC_SoulSicknessPatch_v1_00.esp  (Version 1.00)148  NX9_Guard_LGTrib_patch.ESP149  NX9_Guard_LGRedoran_Patch.ESP150  TC_PuzzleCanol.esp151  DN_1st_Person_bodies.esp152  DN_1st_Person_Armor.esp153  PurchasableAlchemyLab_v_1_00.esp  (Version 1.00)154  Dark Brotherhood Assassins Fix.esp155  DB_Attack_Mod.esp156  Antares' Creatures -  Cecaelia.esp157  Greater Undead.esp158  DX_CreatureAdditionsV1.0.esp159  A_flock_of_seagulls.esp160  Dahrk Creatures I.ESP161  CreaturesLessTownVermin.esp162  Minions of House Dagoth.esp163  Neo's Unique Creatures.esp164  NX9_ghosts_wraiths.ESP165  NX9_liches.esp166  DN-GDRv1_NOM.esp  (Version 1)167  Bloated Caves.esp168  Graphic Herbalism.esp169  Graphic Herbalism Extra.esp170  NOM 2.13.esp  (Version 2.13-02)171  Piratelords Trade Enhancements.esp172  UniqueFinery.esp173  Merged_Objects.esp174  AfterObjectsPTE.esp175  PTE - BC Patch.esp176  House of Mannequins - Mistform fix.esp177  Chargen Revamped Patch 2.1a.esp178  TheForgottenShields - Artifacts_NG.esp179  Census and Excise Office.esp180  Mashed Lists.esp

It could be stencil shadows. If you have high detail shadows and/or an NPC has a shadow mesh that isn't closed properly, the game can slow down hugely trying to calculate the shadow for the holes in that mesh. When an NPC dies the shadow goes away. It's caused by meshes that aren't structured properly by the modeller for casting shadows.

Would a quick test for that be to do: Options -> "Real Time Shadows" -> Off ?