I got Kvatch Rebuilt recently, and when I went to the city to do Oblivion's Main Quest, I found that all of the walls of the city were missing when you were outside the city. I also noticed that the walls in the LOD were doubled and clashing. Is this a load order problem, I mean, I regularly use Boss, or am I just an idiot.
If someone could help out an apparent noob, it would be much appreciated.

Post your load order with Wrye Bash pleases. (Right-click on the File tab and choose 'List Mods,' or use OBMM's View Load Order function from the Import/Export dialog.)

Hi again Tommy, sorry I am such a pain, but here you go:
Oblivion.esm
TR_OoT_Main.esm
MD_Saddle_Master.esm
Cobl Main.esm
TamRes.esm
Oscuro's_Oblivion_Overhaul.esm
Enhanced Daedric Invasion.esm
Kvatch Rebuilt.esm
Better Cities Resources.esm
HorseCombatMaster.esm
ShieldOnBack.esm
Unofficial Oblivion Patch.esp
Oblivion Citadel Door Fix.esp
DLCShiveringIsles.esp
Better Cities .esp
TamRes.esp
ClocksOfCyrodiil.esp
ClocksOfCyrodiil_BC_OBC_OC_OCLR_Vanilla.esp
1HweaponOnBack.esp
DLCHorseArmor.esp
DLCHorseArmor - Unofficial Patch.esp
DLCOrrery.esp
DLCOrrery - Unofficial Patch.esp
DLCSpellTomes.esp
DLCSpellTomes - Unofficial Patch.esp
CapesandCloaks.esp
Hemingweys NPC Capes.esp
Nico's Daes' Rakan Swords.esp
Slof's Horses HA Essential.esp
MD Saddlebags v3.0.esp
DLCThievesDen.esp
DLCThievesDen - Unofficial Patch.esp
DLCThievesDen - Unofficial Patch - SSSB.esp
Cobl Glue.esp
Cobl Tweaks.esp
Oscuro's_Oblivion_Overhaul.esp
Castle_Dunkerlore_V1.esp
Malevolent.esp
TR_Stirk.esp
WOTFH_1.3.esp
DLCBattlehornCastle.esp
DLCBattlehornCastle - Unofficial Patch.esp
DLCFrostcrag.esp
DLCFrostcrag - Unofficial Patch.esp
Knights.esp
Knights - Unofficial Patch.esp
TOTF.esp
RTT.esp
Enhanced Daedric Invasion.esp
ElsweyrAnequina.esp
xuldarkforest.esp
xulStendarrValley.esp
xulTheHeath.esp
XulEntiusGorge.esp
xulFallenleafEverglade.esp
xulColovianHighlands_EV.esp
xulChorrolHinterland.esp
xulBeachesOfCyrodiilLostCoast.esp
xulBravilBarrowfields.esp
xulLushWoodlands.esp
xulAncientYews.esp
xulAncientRedwoods.esp
xulCloudtopMountains.esp
xulArriusCreek.esp
xulPatch_AY_AC.esp
xulRollingHills_EV.esp
xulPantherRiver.esp
xulRiverEthe.esp
xulBrenaRiverRavine.esp
xulImperialIsle.esp
xulBlackwoodForest.esp
xulCheydinhalFalls.esp
xulAspenWood.esp
xulSkingradOutskirts.esp
Fort Akatosh Redux.esp
Cyrodiil Legion Addon.esp
Oblivifall - Ambiant Dungeon SFX.esp
Ring of console.esp
ScriptIcon_Replacer.esp
Cobl Races.esp
bgBalancingEVCore.esp
bgMagicEV.esp
bgBalancingEVOptionalClasses.esp
bgBalancingEVOptionalFangs.esp
bgBalancingEVOptionalMoreEyes.esp
bgBalancingOptionalNPCDiversityKvatchRebuilt, for Wrye Bash.esp
bgIntegrationEV.esp
Cobl Races - Balanced.esp
Better Cities - Full City Defences.esp
Better Cities Full.esp
Better Cities - Unique Landscape Barrowfields.esp
Better Cities - Ruined Tail's Tale.esp
Better Cities - Unique Landscape Chorrol Hinterland.esp
Better Cities - Tears of the Fiend.esp
Better Cities - Unique Landscape Cheydinhal Falls.esp
Better Cities - No LEYAWIIN Flooding.esp
Better Cities - Unique Landscape Skingrad Outskirts.esp
Better Imperial City.esp
Better Imperial City FPS Patch.esp
Better Cities - COBL.esp
Better Cities Full FPS Patch.esp
bgMagicEVShader.esp
Hemingweys Capes.esp
Oblivion Graphics Extender Support.esp
IOM - Kvatch.esp
Heretic Reavers.esp
Heretic Reavers.SoB.esp
IOM - Main Quest.esp
DLCHorseArmor-HC2.2nightmare.esp
Gondorian Ranger.esp
TitanOfEther - Vestments of the Steward-Prince.esp
seanbean.esp
Legion Ranger Addon.esp
Nords With Beards.esp

Not compatible with Kvatch Rebuilt. Pick one or the other.

Oh, how did that get in there, no it is not active when I saw this, I was using Aftermath as a temporary fix, and I forgot to take it out for this order, I'll fix that right now.

ClocksOfCyrodiil.esp <-- remove this as the BC version is a REPLACER

will that fix it?

No. That will fix your double-clock problem though, haha. Removing KA should do the trick for Kvatch. You need to do a clean save if you are still seeing double, haha...

bgBalancingOptionalNPCDiversityKvatchRebuilt, for Wrye Bash.esp <-- this requires Wrye Bash

Lastly...I think... You cannot use RBP with COBL Races. The latter is a stripped-down version of the former, and that is the one you have to drop, if you want to keep Integration, that is...

Arggh, I don't currently have KA active. It was not the problem, I had the issue long before I got KA. I got KA to have a backup in case I couldn't fix KR.

This is probably your problem:

I'm guessing the plugin has conflicts with Kvatch Rebuilt.

Wow, haha, I did not even see that...and I don't know what that is...Is that the entire description?


Edit: That LO kind of needs a bashed patch too, unless you change it a bit...

Well, it didn't do anything to Kvatch Aftermath. The exterior walls, as in looking at it from the road block to stop the Daedra, were visible in KA, unlike in KR, at least, for me.

KA and KR are not the same mod. Just try launching your game after a clean save and see if the duplicates are gone...