You're not using any other mods that affect the DLC, are you? SM Plugin Refurbish and JOG's Official Plugins Unnerfed both alter how you get the quests for the DLC. I suspect you might have JOG's mod lurking in your load order, as that one makes changes to the start of all the DLC except for KotN.
Nope, not having those. I'll paste a copy of the list of mods installed. This is also the load order.
Qarls_Harvest.esm
HrmnsOblivionScriptOptimizationv1.0.esp <- Possible cause.
Unofficial Oblivion Patch.esp
DLCShiveringIsles.esp
Unofficial Shivering Isles Patch.esp
UOP Vampire Aging & Face Fix.esp
DLCHorseArmor.esp
DLCHorseArmor - Unofficial Patch.esp
Compatibility Patch - DLCHorseArmor.esp <- Before this one was installed, it didn't work already, so ignore this one, as the Readme says it's compatible with UOP.
DLCOrrery.esp
DLCOrrery - Unofficial Patch.esp
DLCFrostcrag.esp
DLCFrostcrag - Unofficial Patch.esp
DLCThievesDen.esp
DLCThievesDen - Unofficial Patch.esp
DLCThievesDen - Unofficial Patch - SSSB.esp
DLCVileLair.esp
DLCVileLair - Unofficial Patch.esp
DLCMehrunesRazor.esp
DLCMehrunesRazor - Unofficial Patch.esp
DLCSpellTomes.esp
DLCSpellTomes - Unofficial Patch.esp
Knights.esp
Knights - Unofficial Patch.esp
Qarls_Harvest.esp
AltStart.esp <- Possible cause.
Natural_Weather_HDR_by_Max_Tael.esp
Natural_Vegetation_by_Max_Tael.esp
Natural_Habitat_by_Max_Tael.esp
Natural_Water_by_Max_Tael.esp
Book Jackets Oblivion.esp
VA_BetterGold.esp
Pestilent Afflictions.esp
Battledress.esp
Cliff_BetterLetters.esp
RustyItems.esp
M.O.E. - Hunger Effects.esp
M.O.E. - Lucien Lachance Rumors Fix.esp
M.O.E. - Bone Names and Priced Skull.esp
M.O.E. - Undermined Leveled Gameplay - Creature Edition.esp
SilverwareWeapons.esp
M.O.E. - Undermined Leveled Gameplay - Item Edition.esp
Visually Realistic Deadly Lava.esp
Beautiful People.esp
Wyrmfang.esp
Oblivifall - Ambiant Dungeon SFX.esp
superredguard.esp
Sweeper.esp <- Self created mod, just adds some custom made weapons, does not interfere with anything.
CzBuyToggleNightEye.esp