Here's my load order, if it helps;
Spoiler
Oblivion.esm
TR_OoT_Main.esm
You Are Here.esm
All Natural Base.esm
Francesco's Leveled Creatures-Items Mod.esm
Cobl Main.esm
Mart's Monster Mod.esm
Enhanced Daedric Invasion.esm
CM Partners.esm
Easy_Companion_Share.esm
HorseCombatMaster.esm
Younger Hotter NPC's v1.0.esp
Unofficial Oblivion Patch.esp
DLCShiveringIsles.esp
Unofficial Shivering Isles Patch.esp
LoadingScreens.esp
LoadingScreensAddOn.esp
LoadingScreensSI.esp
Natural_Habitat_by_Max_Tael.esp
All Natural - Real Lights.esp
All Natural.esp
All Natural - SI.esp
AmbientDungeons.esp
AliveWaters.esp
AliveWaters - Koi Addon.esp
AliveWaters - Slaughterfish Addon.esp
Ayleid Loot EXtension.esp
Fatality Cam.esp
P1DseeYouSleep.esp
Purge Cell Buffers - Loading.esp
SI Living Economy.esp
DLCHorseArmor.esp
DLCOrrery.esp
DLCVileLair.esp
DLCMehrunesRazor.esp
AyleidMeteorIronWeaponsBASE.esp
AlternativeLightArmors12.esp
Battledress.esp
ClassyClothingCompendium.esp
DaedricCrescentBlade.esp
LootableLichHelm_Hvy.esp
Rogue Sun's Blood Lust Dress.esp
SickleIrons_RT.esp
SilverwareWeapons.esp
VA_DaedricPriestessArmour.esp
Wyrmfang.esp
LeatherHunterArmour.esp
Daedric Lord Armor.esp
DLCThievesDen.esp
Francesco's Optional Leveled Quests.esp
Francesco's Optional Leveled Arena.esp
Francesco's Optional Files 2.esp
Mart's Monster Mod for Fran.esp
Mart's Monster Mod - Additional Enemy NPC Vars.esp
Mart's Monster Mod - Gems & Gem Dust.esp
Mart's Monster Mod - Hunting & Crafting.esp
Mart's Monster Mod - Durability & Damage.esp
Mart's Monster Mod - Safer Quest Locations.esp
Mart's Monster Mod - Dungeons of MMM.esp
Mart's Monster Mod - More Wilderness Life.esp
Mart's Monster Mod - City Defences.esp
Mart's Monster Mod - Extra Wounding.esp
Mart's Monster Mod - Farm Animals.esp
Mart's Monster Mod - Fran's leveled quests.esp
Ivellon.esp
adTreeHome.esp
AyleidArrows.esp
CDEP_FanaCeya.esp
Fort Baltsine.esp
Gaenor in Dementia.esp
OldCrowInn.esp
RuinsOfBrenfa.esp
Spear_of_Bitter_Mercy.esp
sunk ships.esp
The Ayleid Steps.esp
TR_Stirk.esp
Torynwyll.esp
VOILA - Soldiers of Empire.esp
DLCFrostcrag.esp
Knights.esp
The Lost Spires.esp
Enhanced Daedric Invasion.esp
ElsweyrAnequina.esp
Feldscar.esp
Faregyl.esp
xuldarkforest.esp
xulStendarrValley.esp
xulTheHeath.esp
MMMMWL-TheHeath patch.esp
XulEntiusGorge.esp
xulFallenleafEverglade.esp
LostSpires-Everglade patch.esp
Anequina-Fallenleaf-Patch.esp
xulColovianHighlands_EV.esp
xulBeachesOfCyrodiilLostCoast.esp
xulBravilBarrowfields.esp
xulAncientRedwoods.esp
xulCloudtopMountains.esp
xulBrenaRiverRavine.esp
xulImperialIsle.esp
xulAspenWood.esp
Natural_Vegetation_by_Max_Tael.esp
Harvest [Flora].esp
Harvest [Flora] - DLCFrostcrag.esp
Bag of Holding.esp
Cliff's Shacks Basemants-Radiant AI.esp
DS Less Predictable Respawn.esp
fadingtorches v1.3b.esp
M.O.E. - Lycanthropy and Lichcraft.esp
P1DkeyChain.esp
persuasioncompatable1.8.esp
Quest Award Leveller.esp
Quest Award Leveller - Vile Lair.esp
RealisticForceMedium.esp
SetEssentialActors.esp
SupremeMagicka.esp
SM_ShiveringIsles.esp
MidasSpells.esp
Syc_AtHomeAlchemy.esp
attack and hide medium v2.1.esp
Deadlier Traps.esp
sycHearNoEvil.esp
Enhanced Grabbing.esp
SamVimes's Feint Death.esp
actors_in_charge.esp
_darker_dungeons.esp
CM Partners.esp
CM Partners Extra NPCs.esp
ArianaTrudeaux.esp
_burning_kvatch.esp
Francesco's 10 days respawn time - 1-20 day lenght rescale.esp
SPAWN.esp
Get Wet - just droplets.esp
Capucine'sEyeSelection.esp
Nightshade_Armor_ConflictFree.esp
Alkwynd.esp
Streetvendors.esp
Sunken Chapel.esp
RTBlackEveningDress.esp
Luchaire's Dryad Race for MMM.esp
kdRhazed.esp
PTFallingStars.esp
DarknessHollows.esp
BFG's Enhanced Armory.esp
Weapon Expansion Pack for Oblivion Nthusiasts.esp
Phitt's Phighting Phixes.esp
Creature Damage Fix.esp
Bashed Patch, 0.esp
TR_OoT_Main.esm
You Are Here.esm
All Natural Base.esm
Francesco's Leveled Creatures-Items Mod.esm
Cobl Main.esm
Mart's Monster Mod.esm
Enhanced Daedric Invasion.esm
CM Partners.esm
Easy_Companion_Share.esm
HorseCombatMaster.esm
Younger Hotter NPC's v1.0.esp
Unofficial Oblivion Patch.esp
DLCShiveringIsles.esp
Unofficial Shivering Isles Patch.esp
LoadingScreens.esp
LoadingScreensAddOn.esp
LoadingScreensSI.esp
Natural_Habitat_by_Max_Tael.esp
All Natural - Real Lights.esp
All Natural.esp
All Natural - SI.esp
AmbientDungeons.esp
AliveWaters.esp
AliveWaters - Koi Addon.esp
AliveWaters - Slaughterfish Addon.esp
Ayleid Loot EXtension.esp
Fatality Cam.esp
P1DseeYouSleep.esp
Purge Cell Buffers - Loading.esp
SI Living Economy.esp
DLCHorseArmor.esp
DLCOrrery.esp
DLCVileLair.esp
DLCMehrunesRazor.esp
AyleidMeteorIronWeaponsBASE.esp
AlternativeLightArmors12.esp
Battledress.esp
ClassyClothingCompendium.esp
DaedricCrescentBlade.esp
LootableLichHelm_Hvy.esp
Rogue Sun's Blood Lust Dress.esp
SickleIrons_RT.esp
SilverwareWeapons.esp
VA_DaedricPriestessArmour.esp
Wyrmfang.esp
LeatherHunterArmour.esp
Daedric Lord Armor.esp
DLCThievesDen.esp
Francesco's Optional Leveled Quests.esp
Francesco's Optional Leveled Arena.esp
Francesco's Optional Files 2.esp
Mart's Monster Mod for Fran.esp
Mart's Monster Mod - Additional Enemy NPC Vars.esp
Mart's Monster Mod - Gems & Gem Dust.esp
Mart's Monster Mod - Hunting & Crafting.esp
Mart's Monster Mod - Durability & Damage.esp
Mart's Monster Mod - Safer Quest Locations.esp
Mart's Monster Mod - Dungeons of MMM.esp
Mart's Monster Mod - More Wilderness Life.esp
Mart's Monster Mod - City Defences.esp
Mart's Monster Mod - Extra Wounding.esp
Mart's Monster Mod - Farm Animals.esp
Mart's Monster Mod - Fran's leveled quests.esp
Ivellon.esp
adTreeHome.esp
AyleidArrows.esp
CDEP_FanaCeya.esp
Fort Baltsine.esp
Gaenor in Dementia.esp
OldCrowInn.esp
RuinsOfBrenfa.esp
Spear_of_Bitter_Mercy.esp
sunk ships.esp
The Ayleid Steps.esp
TR_Stirk.esp
Torynwyll.esp
VOILA - Soldiers of Empire.esp
DLCFrostcrag.esp
Knights.esp
The Lost Spires.esp
Enhanced Daedric Invasion.esp
ElsweyrAnequina.esp
Feldscar.esp
Faregyl.esp
xuldarkforest.esp
xulStendarrValley.esp
xulTheHeath.esp
MMMMWL-TheHeath patch.esp
XulEntiusGorge.esp
xulFallenleafEverglade.esp
LostSpires-Everglade patch.esp
Anequina-Fallenleaf-Patch.esp
xulColovianHighlands_EV.esp
xulBeachesOfCyrodiilLostCoast.esp
xulBravilBarrowfields.esp
xulAncientRedwoods.esp
xulCloudtopMountains.esp
xulBrenaRiverRavine.esp
xulImperialIsle.esp
xulAspenWood.esp
Natural_Vegetation_by_Max_Tael.esp
Harvest [Flora].esp
Harvest [Flora] - DLCFrostcrag.esp
Bag of Holding.esp
Cliff's Shacks Basemants-Radiant AI.esp
DS Less Predictable Respawn.esp
fadingtorches v1.3b.esp
M.O.E. - Lycanthropy and Lichcraft.esp
P1DkeyChain.esp
persuasioncompatable1.8.esp
Quest Award Leveller.esp
Quest Award Leveller - Vile Lair.esp
RealisticForceMedium.esp
SetEssentialActors.esp
SupremeMagicka.esp
SM_ShiveringIsles.esp
MidasSpells.esp
Syc_AtHomeAlchemy.esp
attack and hide medium v2.1.esp
Deadlier Traps.esp
sycHearNoEvil.esp
Enhanced Grabbing.esp
SamVimes's Feint Death.esp
actors_in_charge.esp
_darker_dungeons.esp
CM Partners.esp
CM Partners Extra NPCs.esp
ArianaTrudeaux.esp
_burning_kvatch.esp
Francesco's 10 days respawn time - 1-20 day lenght rescale.esp
SPAWN.esp
Get Wet - just droplets.esp
Capucine'sEyeSelection.esp
Nightshade_Armor_ConflictFree.esp
Alkwynd.esp
Streetvendors.esp
Sunken Chapel.esp
RTBlackEveningDress.esp
Luchaire's Dryad Race for MMM.esp
kdRhazed.esp
PTFallingStars.esp
DarknessHollows.esp
BFG's Enhanced Armory.esp
Weapon Expansion Pack for Oblivion Nthusiasts.esp
Phitt's Phighting Phixes.esp
Creature Damage Fix.esp
Bashed Patch, 0.esp
EDIT: It seems to be save-game related, as the problem mostly occurs with my Level 12 character.