However now I'm running the newer versions of OOO/MMM and FCOM these changes have dissapeared.
I've used the new OMOD MMM installer which alters the BSA files as well, so I don't think that's the issue.
LoadOrder- if there are any issues please let me know.
Spoiler
Oblivion.esm
Francesco's Leveled Creatures-Items Mod.esm
Francesco's Optional New Items Add-On.esm
Francesco's Optional New Creatures Add-On.esm
Cobl Main.esm
Oscuro's_Oblivion_Overhaul.esm
Mart's Monster Mod.esm
FCOM_Convergence.esm
Unofficial Oblivion Patch.esp
DLCShiveringIsles.esp
Unofficial Shivering Isles Patch.esp
Francesco's Optional Chance of Stronger Bosses.esp
Francesco's Optional Chance of Stronger Enemies.esp
Francesco's Optional Chance of More Enemies.esp
Francesco's Optional Leveled Guards.esp
FCOM_Francescos.esp
FCOM_FrancescosItemsAddOn.esp
FCOM_FrancescosNamedBosses.esp
Oblivion Graphics Extender Support.esp
DLCHorseArmor.esp
DLCOrrery.esp
DLCVileLair.esp
DLCMehrunesRazor.esp
DLCSpellTomes.esp
DLCThievesDen.esp
Cobl Glue.esp
Cobl Si.esp
Bob's Armory Oblivion.esp
FCOM_BobsArmory.esp
Oblivion WarCry EV.esp
FCOM_WarCry.esp
Oscuro's_Oblivion_Overhaul.esp
OOO 1.32-Cobl.esp
Mart's Monster Mod - Additional Enemy NPC Vars.esp
FCOM_Convergence.esp
FCOM_RealSwords.esp
Mart's Monster Mod - More Wilderness Life.esp
Mart's Monster Mod - More Passive Wildlife.esp
Mart's Monster Mod - Extra Wounding.esp
Mart's Monster Mod - Dungeons of MMM.esp
Mart's Monster Mod - Gems & Gem Dust.esp
Mart's Monster Mod - Hunting & Crafting.esp
Mart's Monster Mod - Farm Animals.esp
Mart's Monster Mod - Diverse WaterLife.esp
Mart's Monster Mod - Slof Horses Complete.esp
Mart's Monster Mod - Diverse Runeskulls Loot G&GD.esp
Mart's Monster Mod - Shivering Isles.esp
OOO-WaterFish.esp
MMM-Cobl.esp
DLCFrostcrag.esp
Knights.esp
FCOM_Knights.esp
Salmo the Baker, Cobl.esp
Francesco's Slower skills x1.5.esp
Mart's Monster Mod - Resized Races.esp
Francesco's 10 days respawn time - 1-20 day lenght rescale.esp
Cobl Silent Equip Misc.esp
Bashed Patch, 0.esp
Merged Patch.esp
Francesco's Leveled Creatures-Items Mod.esm
Francesco's Optional New Items Add-On.esm
Francesco's Optional New Creatures Add-On.esm
Cobl Main.esm
Oscuro's_Oblivion_Overhaul.esm
Mart's Monster Mod.esm
FCOM_Convergence.esm
Unofficial Oblivion Patch.esp
DLCShiveringIsles.esp
Unofficial Shivering Isles Patch.esp
Francesco's Optional Chance of Stronger Bosses.esp
Francesco's Optional Chance of Stronger Enemies.esp
Francesco's Optional Chance of More Enemies.esp
Francesco's Optional Leveled Guards.esp
FCOM_Francescos.esp
FCOM_FrancescosItemsAddOn.esp
FCOM_FrancescosNamedBosses.esp
Oblivion Graphics Extender Support.esp
DLCHorseArmor.esp
DLCOrrery.esp
DLCVileLair.esp
DLCMehrunesRazor.esp
DLCSpellTomes.esp
DLCThievesDen.esp
Cobl Glue.esp
Cobl Si.esp
Bob's Armory Oblivion.esp
FCOM_BobsArmory.esp
Oblivion WarCry EV.esp
FCOM_WarCry.esp
Oscuro's_Oblivion_Overhaul.esp
OOO 1.32-Cobl.esp
Mart's Monster Mod - Additional Enemy NPC Vars.esp
FCOM_Convergence.esp
FCOM_RealSwords.esp
Mart's Monster Mod - More Wilderness Life.esp
Mart's Monster Mod - More Passive Wildlife.esp
Mart's Monster Mod - Extra Wounding.esp
Mart's Monster Mod - Dungeons of MMM.esp
Mart's Monster Mod - Gems & Gem Dust.esp
Mart's Monster Mod - Hunting & Crafting.esp
Mart's Monster Mod - Farm Animals.esp
Mart's Monster Mod - Diverse WaterLife.esp
Mart's Monster Mod - Slof Horses Complete.esp
Mart's Monster Mod - Diverse Runeskulls Loot G&GD.esp
Mart's Monster Mod - Shivering Isles.esp
OOO-WaterFish.esp
MMM-Cobl.esp
DLCFrostcrag.esp
Knights.esp
FCOM_Knights.esp
Salmo the Baker, Cobl.esp
Francesco's Slower skills x1.5.esp
Mart's Monster Mod - Resized Races.esp
Francesco's 10 days respawn time - 1-20 day lenght rescale.esp
Cobl Silent Equip Misc.esp
Bashed Patch, 0.esp
Merged Patch.esp