I recently donwloaded Kvatch aftermath and I fear this may be the problem. however, I unchecked it and the gates still arent there, yet NPC's come out of where the gates should be.
Load order:

Oblivion.esmGTAesgaard_2.esmTR_OoT_Main.esmHammerfell.esmJog_X_Mod.esmCobl Main.esmTamRes.esmOscuro's_Oblivion_Overhaul.esmCyrodiilUpgradeResourcePack.esmArmamentarium.esmBetter Cities Resources.esmCURP_Controller.esmVVAdvanced.esmCLS-Craftybits.esmTantrivayliaChimer.esmCM Partners.esmHorseCombatMaster.esmToaster Says Share v3.esmDLCShiveringIsles.espBetter Cities .espTamRes.espNatural_Weather_HDR_by_Max_Tael.espNatural_Habitat_by_Max_Tael.espEnhanced Water v2.0 HD.espValenwood.espAkatosh Mount By Saiden Storm.espBook Jackets Oblivion.espCNRP Bruma4OOO.espCNRP Cheydinhal4OOO.espCNRP Chorrol4OOO.espP1DseeYouSleep.espPortable Campsite - Quickstart.espP1DseeYouSleep - Portable Campsite - Quickstart.espQ - More and Moldy Ingredients v1.1.espMap Marker Overhaul.espMap Marker Overhaul - SI additions.espDLCHorseArmor.espDLCHorseArmor - Unofficial Patch.espDLCOrrery.espDLCOrrery - Unofficial Patch.espDLCVileLair.espDLCVileLair - Unofficial Patch.espP1DseeYouSleep - DLCVileLair.espDLCMehrunesRazor.espDLCMehrunesRazor - Unofficial Patch.espDLCSpellTomes.espDLCSpellTomes - Unofficial Patch.esp1AzuSeraphimSet.espArmory of the Silver Dragon.espCapesandCloaks.espDMACArmor.espNew Frostmourne Sword by Jojjo v1_0.espRingwraithArmorDaedric.espSilverlight Armor by Jojjo.esptda_Armoury.esptda_WitchKingHelm.espThieves Arsenal.espAL_AuroranBattleSteed.espDLCThievesDen.espDLCThievesDen - Unofficial Patch.espDLCThievesDen - Unofficial Patch - SSSB.espExnemRuneskulls.espCobl Glue.espCobl Si.espOOO 1.32-Cobl.espCobl Tweaks.espVVAdvanced.espVVAdvanced-SI.espP1DseeYouSleep - VVAdvanced.espOscuro's_Oblivion_Overhaul.espOOO-Water_Weeds.espArmamentariumLLVendors.espArmamentariumArtifacts.espArmamentariumLL4OOO.espArmamentariumLLMagicOOO.espCastle Ravenpride.espBHC_Expanded.espdelivery_job.espDelivery Job - BC.espGTAesgaard_2.espJQ-AssassinQuest.espKragenir's Death Quest.espEiAmod.espEiAmod_ShiveringIsles.espbladesfactionmod.espReturn Of Shadows.espScribe Supplies.espServant of the Dawn.espTantrivaylia.espThe Crimson Queen.espTheElderCouncil.espTheElderCouncil_TempleOfTheOne.espthievery.espTR_Stirk.espStirk_Compatibility_Patch.espVaultsofCyrodiilBC.espDLCFrostcrag.espFrostcragRebornCobl.espKnights.espKnights - Unofficial Patch.espUngarion1TheWelkyndSword.espHoarfrostCastle.espSummerset.espReaper's Esmeralda's Desert Manor.espFort Akatosh Redux.espNatural_Vegetation_by_Max_Tael.espHarvest [Flora].espHarvest [Flora] - Shivering Isles.espKyoma's Journal Mod.espCLS-Craftybits.espAlternative Start by Robert Evrae.espMidasSpells.espEnhanced Grabbing.espimmersive_caves_auto.espAssassins Creed - Altair's Gear - Heavy Armor.espCM Partners.espCM Partners Special NPCs.espCM Partners NPC.espCM Partners More NPCs.espCM Partners Marker NPCs.espCM Partners Extra NPCs.espBetter Cities - Full City Defences.espBetter Cities Full.espBetter Cities - Thievery.espBetter Imperial City.espBetter Imperial City FPS Patch.espBetter Cities - COBL.espBetter Cities Full FPS Patch.espReal Lava 1.3.espViconia.espgreenemprobe.espfreezeremover.espCastleHeiLi.espRimmen.espRimmen Market Place.espValenwood_Anequina_Patch.espElsweyrAnequina.espToaster Says Share Faction Recruitment.espRTT.esp1em_Vilja.espKvatchAftermath.espSoT_TheOrderofNibenay.espDeadlyReflex 5 - Combat Moves.espSI - Skywatch.espSide's Sailing Ships.espColored Map for Elsweyr 1.1.esp

tried it with no mods. Still didn't work. Reinstalled Oblivion, Shivering Isles, Knights, and the official plugins and it still didnt work. opened it in the CS and found that the door is there and seems to be fine in the CS. No error messages there, by the way. Reloaded it with Kvatch Aftermath and found one error message where it said something like "Reference fence post is attached to the wrong cell" or something. it did mention the cell as Kvatch. But nothing about a door. And the dorr was there and so were many buildings. I guess none of the buildings show up either. What is happening?

Hmm you said you installed Kvatch Aftermath? Well I think there is a guy named Mr. Fix It (or somewhere along those lines) that uninstalls the mod then you just have to disable it yourself. I'm not sure if this will help since I have no idea where this guy is. I know there was one for Origin of the Mages guild, TEC, and Kvatch Rising so I'm hoping the mod author had always done that with his mods.

I suggest that if you're going to install a Kvatch rebuilt mod to do so after you have done everything there. Close the gate, rescue the people in the chapel, and take back the castle just to be on the safe side. But it's a little too late to say that.

Oh and one more thing. Are you using BOSS to sort all those mods into a load order that will prevent conflicts? Because there could be a conflict or something.

I had the same problem after installing & playing MOE (think that's the name..the one that lets you play cyrodiil before the MQ-great mod but...) I had to do a reinstall to get back my game...then kept strict eye on what save was MOEd & what save wasn't..Sorry

Yes I use BOSS but some things I have to manually change that BOSS doesn't catch. Like some thing HAS to be loaded after any other map changing mods and BOSS doesnt put it last, its put it last on the known mods section.
Anyway, The city itself works, everythings great inside. i just have to cow in every time. but nothing extremely game breaking, just immersion breaking.