This also seems to be the only game being affected by this, Morrowind, Fallout 3, etc. do not suffer from this problem.
If it helps, here's my Mod LO, but I doubt they are the problem, since I was able to replicate the loading slowdown on a Vanilla install:
You know, I think the moment I can afford it, I'm gonna ditch Steam and get a disc copy to see if that helps any.
Spoiler
Active Mod Files:00 Oblivion.esm01 TR_OoT_Main.esm02 All Natural Base.esm [Version 1.0]03 Cobl Main.esm [Version 1.73]04 Oscuro's_Oblivion_Overhaul.esm [Version 1.34]05 Mart's Monster Mod.esm [Version 3.7b3p3]06 Mart's Monster Mod for OOO.esm [Version 0.9.9MB3]07 Kvatch Rebuilt.esm08 Better Cities Resources.esm [Version 4.7.1]09 Progress.esm [Version 2.2]0A Unofficial Oblivion Patch.esp [Version 3.2.10]0B Oblivion Citadel Door Fix.esp0C DLCShiveringIsles.esp0D Unofficial Shivering Isles Patch.esp [Version 1.4.0]0E Better Cities .esp0F All Natural.esp [Version 1.0]10 All Natural - SI.esp [Version 1.0]++ All Natural - Bravil Mages Fix.esp++ All Natural - SI Settlements NIW Support.esp11 Enhanced Water v2.0 HD.esp++ Enhanced Water v2.0 HD - SI Addon.esp [Version 0.1]++ Symphony of Violence.esp12 Rainbows.esp13 All Natural - Real Lights.esp [Version 1.0]14 Akatosh Mount By Saiden Storm.esp++ Item interchange - Extraction.esp [Version 0.78]15 kuerteeSittableRocks.esp16 Enhanced Economy.esp [Version 4.2.1]17 Duke Patricks - Friendship Ring For Companion Detection.esp [Version 1.8]18 Enhanced Hotkeys.esp [Version 1.2]19 DLCHorseArmor.esp1A DLCHorseArmor - Unofficial Patch.esp [Version 1.0.5]1B DLCOrrery.esp1C DLCOrrery - Unofficial Patch.esp [Version 1.0.3]1D DLCVileLair.esp1E DLCVileLair - Unofficial Patch.esp [Version 1.0.5]1F DLCMehrunesRazor.esp20 DLCMehrunesRazor - Unofficial Patch.esp [Version 1.0.4]21 DLCSpellTomes.esp++ DLCSpellTomes - Unofficial Patch.esp [Version 1.0.1]22 DLCThievesDen.esp23 DLCThievesDen - Unofficial Patch.esp [Version 1.0.5]24 DLCThievesDen - Unofficial Patch - SSSB.esp [Version 1.0.4]25 Cobl Glue.esp [Version 1.73]26 Cobl Si.esp [Version 1.63]++ Cobl Tweaks.esp [Version 1.73]27 Oscuro's_Oblivion_Overhaul.esp [Version 1.34]28 OOO 1.32-Cobl.esp [Version 1.72]29 Mart's Monster Mod for OOO.esp [Version 0.9.9MB3]++ Mart's Monster Mod - Shivering Isles.esp [Version 3.7b3p3]++ Mart's Monster Mod - Looting NPCs & Creatures.esp [Version 3.7b3p3]++ Mart's Monster Mod - Less Bone Loot.esp [Version 3.7b3p3]++ Mart's Monster Mod - Less Rats.esp [Version 3.7b3p3]++ Mart's Monster Mod for OOO - LessReaversInGates.esp [Version 0.9.9MB3]++ Mart's Monster Mod - No Balrogs.esp [Version 3.7b3p3]++ Mart's Monster Mod - Spawn Rates - Reduced.esp [Version 3.7b3p3]2A Mart's Monster Mod - Safer Quest Locations.esp [Version 3.7b3p3]2B Mart's Monster Mod - More Wilderness Life.esp [Version 3.7b3p3]++ Mart's Monster Mod - Friendlier Factions OOO.esp [Version 3.7b3p3]2C Mart's Monster Mod - Farm Animals.esp [Version 3.7b3p3]2D Mart's Monster Mod - Diverse WaterLife.esp [Version 3.7b3p3f]++ MMM-Cobl.esp [Version 1.73]2E Kvatch Rebuilt.esp++ Kvatch Rebuilt - OOO Compatibility.esp2F Kvatch Rebuilt Weather Patch.esp30 TR_Stirk.esp31 DLCBattlehornCastle.esp32 DLCBattlehornCastle - Unofficial Patch.esp [Version 1.0.4]33 DLCFrostcrag.esp34 FrostcragRebornCobl.esp35 Knights.esp36 Knights - Unofficial Patch.esp [Version 1.0.10]++ Mart's Monster Mod for OOO - Knights .esp [Version 0.9.9MB3]37 The Lost Spires.esp38 MannimarcoRevisited.esp39 MannimarcoRevisitedOOO.esp [Version 0.1]3A road+bridges.esp [Version 4.5.8]3B xuldarkforest.esp [Version 1.0.4]3C LostSpires-DarkForest patch.esp3D xulStendarrValley.esp [Version 1.2.2]3E xulTheHeath.esp3F MMMMWL-TheHeath patch.esp40 XulEntiusGorge.esp41 xulFallenleafEverglade.esp [Version 1.3.1]42 LostSpires-Everglade patch.esp [Version 1.2]43 Anequina-Fallenleaf-Patch.esp44 xulColovianHighlands_EV.esp [Version 1.2.1]45 xulChorrolHinterland.esp [Version 1.2.2]46 xulBeachesOfCyrodiilLostCoast.esp [Version 1.6.4]47 xulBravilBarrowfields.esp [Version 1.3.2]48 xulLushWoodlands.esp [Version 1.3]49 xulAncientYews.esp [Version 1.4.3]4A xulAncientRedwoods.esp [Version 1.6]4B xulCloudtopMountains.esp [Version 1.0.3]4C xulArriusCreek.esp [Version 1.1.3]4D xulPatch_AY_AC.esp [Version 1.1]4E xulRollingHills_EV.esp [Version 1.3.2]4F MMMMWL-RollingHills patch.esp50 xulPantherRiver.esp51 xulRiverEthe.esp [Version 1.0.2]52 xulBrenaRiverRavine.esp [Version 1.1]53 xulImperialIsle.esp [Version 1.6.3]54 xulBlackwoodForest.esp [Version 1.1.0]55 xulCheydinhalFalls.esp [Version 1.0.1]56 KvatchRebuilt-CheydinhalFalls patch.esp57 xulAspenWood.esp [Version 1.0.2]58 xulSkingradOutskirts.esp [Version 1.0.1]59 xulSnowdale.esp [Version 1.0]5A FrostcragReborn-Snowdale patch.esp5B SnowdaleOOOPatch.esp5C NRB4+UL-II Patch.esp [Version 5.0.1]5D Harvest [Flora].esp [Version 3.0.0]++ Harvest [Flora] - Shivering Isles.esp [Version 3.0.0]++ Harvest [Flora] - DLCVileLair.esp [Version 3.0.0]5E Harvest [Flora] - DLCFrostcrag.esp [Version 3.0.0]5F kuerteeInventoryIsABackpack.esp60 RealisticFatigue.esp61 RealSleepExtended.esp [Version 2.5]62 SupremeMagicka.esp [Version 0.89]63 SM_ShiveringIsles.esp [Version 0.86]++ SM_DLCSpellTome.esp [Version 0.80]++ SM_OOO.esp [Version 0.89]++ SM_MMM.esp [Version 0.89]++ SM_COBL.esp [Version 0.86]64 SM_EnchantStaff.esp [Version 0.80]++ SM_UnlockSpells.esp [Version 0.70]++ SM_Scrolls.esp [Version 0.84]++ SM_SigilStone.esp [Version 0.83]65 SM Bounty.esp [Version 1.22c]++ CoblDeathFix.esp [Version 1.20]66 Duke Patricks - Actors Can Miss Now.esp67 nGCD.esp68 nGCD Oghma Infinium.esp++ nGCD Skeleton Key.esp69 actors_in_charge.esp** Let There Be Darkness - Cyrodiil + SI.esp** Let There Be Darkness - Knights.esp** Let There Be Darkness - Mehrunes Razor.esp** Let There Be Darkness - Thieves Den.esp** Let There Be Darkness - OOO.esp** Let There Be Darkness - Kvatch Rebuilt.esp** Let There Be Darkness - Lost Spires.esp** Let There Be Darkness - UL Colovian Highlands.esp** Let There Be Darkness - UL Lost Coast.esp** Let There Be Darkness - UL Brena.esp** Let There Be Darkness - UL Blackwood Forest.esp++ Item interchange - Placement.esp [Version 0.78]++ Item interchange - Placement for Frostcrag Reborn.esp [Version 0.78]6A Cobl Races.esp [Version 1.52]++ Cobl Races - Balanced.esp [Version 1.52]6B Better Cities Full.esp [Version 4.7.0]6C Better Cities - Unique Landscape Barrowfields.esp [Version 4.7.0]6D Better Cities - Unique Landscape Chorrol Hinterland.esp [Version 4.7.0]6E Better Cities - Unique Landscape Cheydinhal Falls.esp [Version 4.7.0]6F Better Cities - Unique Landscape Skingrad Outskirts.esp70 Better Imperial City.esp [Version 4.7.0]71 Better Imperial City FPS Patch.esp [Version 4.7.0]72 Better Cities - COBL.esp [Version 2.1]73 Better Cities Full FPS Patch.esp [Version 4.7.0]74 Enhanced Economy - Soulgems.esp [Version 4.2.1]75 Real Hunger, Cobl.esp [Version 1.6.1]** NRB4 Standard Road Record.esp++ Cobl Filter Late MERGE ONLY.esp [Version 1.53]** All Natural - Indoor Weather Filter For Mods.esp [Version 1.0]76 Bashed Patch, 0.esp77 Duke Patricks - Combat Archery.esp [Version 3.3]78 MergedMaps.esp79 FormID Finder4.esp7A Streamline 3.1.esp