'eyyy. So apparently I have a mod that is making some strange changes to heavy armor. It's giving me a penalty to my speed and agility, something I don't remember ever having in the vanilla game. Problem is, I have no idea which mod it is.

So is this something vanilla and I'm just crazy, or is it one of my mods? Here's my load order.

GameFile0=Better Heads Bloodmoon addon.esm
GameFile1=Better Heads Tribunal addon.esm
GameFile2=Better Heads.esm
GameFile3=Bloodmoon Landscape Overhaul 1.0.esm
GameFile4=Bloodmoon.esm
GameFile5=Clean The Lost Artifacts of Morrowind.esm
GameFile6=GDR_MasterFile.esm
GameFile7=Hilgya the Seamstress.esm
GameFile8=Morrowind Patch v1.6.4.esm
GameFile9=Morrowind.esm
GameFile10=Pocket Pals - Names!.esm
GameFile11=Pocket Pals Skill Base.esm
GameFile12=Rise of House Telvanni.esm
GameFile13=Texture Fix 1.8.esm
GameFile14=Tribunal.esm
GameFile15=TR_Data.esm
GameFile16=TR_Map1.esm
GameFile17=TR_Map2.esm
GameFile18=100ProjectileStoreChance.esp
GameFile19=abotGuars.esp
GameFile20=acsSaviorArmor.esp
GameFile21=adamantiumarmor.esp
GameFile22=All Silt Strider Ports.esp
GameFile23=almalexia armor.esp
GameFile24=Alternate Messages V1.4.esp
GameFile25=AreaEffectArrows.esp
GameFile26=Astion's Chrysamere.esp
GameFile27=Atmospheric Balmora for VBAnIW.ESP
GameFile28=Authentic Signs IT 1.1.esp
GameFile29=Balmora Council Club.esp
GameFile30=BB Dark Brotherhood by Westly.esp
GameFile31=bcsounds.esp
GameFile32=BD_itemShare.esp
GameFile33=Better Bodies.esp
GameFile34=Better Clothes_v1.1.esp
GameFile35=Better Moon and Star.esp
GameFile36=Better Skulls.ESP
GameFile37=BetterBooks_AlchFormfix.esp
GameFile38=Boe_lich_particle.esp
GameFile39=Book Jackets - Bloodmoon.esp
GameFile40=Book Jackets - Morrowind.esp
GameFile41=Book Jackets - Tribunal.esp
GameFile42=carts!.ESP
GameFile43=Charming Ash Vampires.ESP
GameFile44=Cjad's Templar Pauldron Fix.ESP
GameFile45=Clean Better Caldera.esp
GameFile46=Clean Ebonheart Interior Expansion.esp
GameFile47=Clean Restored Artifacts.esp
GameFile48=Clean Royal Chargen.esp
GameFile49=Clean The Masks of the Gods.esp
GameFile50=Clean To Serve Sithis_.esp
GameFile51=Clean Weapon Sheaths Ultimate.esp
GameFile52=ComprehensiveChargen.esp
GameFile53=correctUV Ore Replacer 1.0.esp
GameFile54=Creatures.esp
GameFile55=Creeper's Quest.esp
GameFile56=DB_Attack_Mod3.esp
GameFile57=Detect Owner.esp
GameFile58=Dirnae's Slower Walk.ESP
GameFile59=Divayth Fyr's Bribe.esp
GameFile60=DN-GDRv1.esp
GameFile61=DN_Adamantium.esp
GameFile62=dracandrosvoice.esp
GameFile63=DreadKnight.ESP
GameFile64=Dura gra-Bol's House Extended.ESP
GameFile65=Dwemer Sentinel.esp
GameFile66=DynamicMagickaRegeneration-2.1-Tribunal.esp
GameFile67=EBQ_Artifact.esp
GameFile68=em_armor_mod_Morr_short.esp
GameFile69=entertainers.esp
GameFile70=ExpandedBirthsigns4Purists.esp
GameFile71=Firemoth Expanded 1.5.esp
GameFile72=Flee AI Tweaks.esp
GameFile73=Fligg's Slave Mod.esp
GameFile74=frostmoth_repaired_v0_31.esp
GameFile75=Gothelittles_Legion_Guides.esp
GameFile76=Grave Goods.esp
GameFile77=Guarded GhostGate.esp
GameFile78=Healing.esp
GameFile79=height rebalancing.esp
GameFile80=Hide The Skooma.esp
GameFile81=Hilgya the Seamstress Expansion 1.esp
GameFile82=Holy King Armor.esp
GameFile83=HospitalityPapers.esp
GameFile84=Illuminated Order v1.0 - Bloodmoon Compatibility Extras.esp
GameFile85=Illuminated Order v1.0.esp
GameFile86=Illuminated Windows - Bloodmoon.esp
GameFile87=Illuminated Windows.esp
GameFile88=Imperial Chain Boots n Gauntlets.ESP
GameFile89=Imperial Contraband.esp
GameFile90=ImprovedFollowers.esp
GameFile91=It's me, you idiot.esp
GameFile92=Jiub Companion 1.3.esp
GameFile93=Juniper's Twin Lamps (1.1 Tribunal).esp
GameFile94=Kalian's Hairs.esp
GameFile95=KS_Ren's_Oblivion_Hair_for_Morrowind_1.0.esp
GameFile96=k_in_tent.esp
GameFile97=k_weather.esp
GameFile98=LAMW_GDRv1_Patch.esp
GameFile99=LA_MWSE Addon.esp
GameFile100=LGNPC_Aldruhn_v1_20.esp
GameFile101=LGNPC_Aldruhn_v1_20_suppl.esp
GameFile102=LGNPC_AldVelothi_v1_20.esp
GameFile103=LGNPC_GnaarMok_v1_10.esp
GameFile104=LGNPC_HlaOad_v1_32.esp
GameFile105=LGNPC_IndarysManor_v1_51.esp
GameFile106=LGNPC_Khuul_v2_10.esp
GameFile107=LGNPC_MaarGan_v1_20.esp
GameFile108=LGNPC_NoLore_v0_83.esp
GameFile109=LGNPC_PaxRedoran_v1_20.esp
GameFile110=LGNPC_Pelagiad_v1_22.esp
GameFile111=Lgnpc_SN.esp
GameFile112=LGNPC_SoulSicknessPatch_v1_00.esp
GameFile113=LGNPC_TelMora_v1_20.esp
GameFile114=LGNPC_TelUvirith_v1_20.esp
GameFile115=LGNPC_TelUvirith_v1_20_UI.esp
GameFile116=LGNPC_VivecFQ_v2_10.esp
GameFile117=LGNPC_VivecRedoran_v1_50.esp
GameFile118=Lich King.esp
GameFile119=master_index.esp
GameFile120=Merchant Investments.esp
GameFile121=MW_Public_Library.esp
GameFile122=New Argonian Bodies - Clean.esp
GameFile123=New Khajiit Bodies - Clean.esp
GameFile124=New Suran.esp
GameFile125=NOSEAMODAIPLATUE.ESP
GameFile126=NX9Guards_Imperial_1.2.esp
GameFile127=Odai-Cascade V2.5.esp
GameFile128=OT_Vivec Beta 0.6b.esp
GameFile129=Painkiller's Lucky Coin.esp
GameFile130=Passive_Healthy_Wildlife.esp
GameFile131=Pearls Enhanced - Colored Pearls Add-on.ESP
GameFile132=Pocket Pals - Dwemer Mechs!.esp
GameFile133=Pocket Pals - Mournhold Mayhem!.esp
GameFile134=Prison Moon Enhanced.esp
GameFile135=Psy_UniqueDremora_T.esp
GameFile136=Psy_VivecGodReplacer.esp
GameFile137=Psy_VivecGodReplacer_Tribunal.esp
GameFile138=Riptides Face & Clothing Replace Final.esp
GameFile139=Sewer Hideout.esp
GameFile140=sg1_vitelius_estate.esp
GameFile141=Silt Striders in the Wild.esp
GameFile142=Silver Weapon Crate Fix.esp
GameFile143=Sol-Weather Tweak.esp
GameFile144=Soti_BetterDreamers.esp
GameFile145=Sotonhorian.ESP
GameFile146=Suran_Underworld_2.5.esp
GameFile147=The Undead Dungeons.esp
GameFile148=The Imperial Legion Badge.esp
GameFile149=The Neverhalls.esp
GameFile150=The Ultimate Knight Shop.esp
GameFile151=TheForgottenShields - Artifacts_NG.esp
GameFile152=Tireless running.esp
GameFile153=TLM - Complete.esp
GameFile154=TravelingMerchants-1.2_BETA.esp
GameFile155=TribIntegration.esp
GameFile156=TR_CensusAndExciseTravel.esp
GameFile157=t_lostheir.esp
GameFile158=UL_MWSE_patch.esp
GameFile159=UL_RoHT_1.3_Compatibility.esp
GameFile160=UL_TLM_ambiance.esp
GameFile161=Unique Ghosts - M - T.esp
GameFile162=UniqueFinery.esp
GameFile163=Uvirith's Legacy Book Jackets Add-on.esp
GameFile164=Uvirith's Legacy_BETA1.10.esp
GameFile165=Vality's Ascadian Isles Addon.esp
GameFile166=Vality's Balmora Addon.esp
GameFile167=Vality's Bitter Coast Addon.esp
GameFile168=Vivec Expansion 2.0.esp
GameFile169=vn_goldweight.esp
GameFile170=Waterfall v1.0.esp
GameFile171=WA_Signy_Signposts(!)_TR.ESP
GameFile172=WeatheredSigns.esp
GameFile173=Westly's Breton Male Headpack.esp
GameFile174=Xenn's Strict Factions.ESP
GameFile175=Yagrum Advanced 2.0.esp

TLM Complete, check the readme for it. It modifies sneak and combat attributes when wearing heavier armour, unfortunately it doesn't take skill into account much.

I was just going through the readme, actually. At least, for the modular version it doesn't seem to have the esp that adds the armor penalties marked there (I crtl-f'd "Heavy Armor".) Do you have any idea which esp I need to leave out when I switch to modular, then?

It's not that modular, it's integrated with Sneak Modifiers. You should be able to cut the penalties down by editing the _TLM_ArmorCalc script. Set the unwanted penalties at the bottom to zero.

Where do I need to go to modify this script?

Open TLM - Complete.esp in TESCS. Click Set as Active File.
Gameplay menu > Edit Scripts...
Click open button, select _TLM_ArmorCalc from the list.
Scroll down to the bottom and set penalties you want to turn off to 0.