That does not sound right.
I meant the initialization is long but it is done in one single frame!
When you first come from the gate after installing the mod, when you are somewhere by the Flowing Bowl door, the initialization will trigger, the game will freeze for 1-2 seconds and that is it! No more initialization ever.
After that is just the normal rocking script, which may or may not be the cause of your lag.
If it is the culprit, it wont get any better (or worse) as time goes by.
Ok, I see what you're say about a single frame initialization. I noticed it right at the point where the screenshot was taken below. It was a slight stutter and immediately after I saw the ships start to rock up an down, but then only a second or two later the sever lag took place. Again, it's as if my frame rate drops to 1 frame or less. I can get video of it as well if needed.
Here is a http://img38.imagefra.me/img/img38/2/2/10/far327/f_13t1pwkp5clm_630e11f.png of an error message that popped up after waiting for the lag to end. I waited about 5 minutes before the error message appeared.
I'll try loading the mod after my bashed patch next to see if I get different results. This time I'll open the game in a window so I can watch the CPU usage.
Active Mod Files:00 Oblivion.esm01 Morrowind_ob.esm02 Tribunal_ob.esm03 Bloodmoon_ob.esm04 All Natural Base.esm [Version 0.9.8]05 Francesco's Leveled Creatures-Items Mod.esm06 Francesco's Optional New Items Add-On.esm07 Oscuro's_Oblivion_Overhaul.esm [Version 1.34]08 Mart's Monster Mod.esm [Version 3.7b3p3]09 FCOM_Convergence.esm [Version 0.9.9MB3]0A Armamentarium.esm [Version 1.35]0B Artifacts.esm0C Better Cities Resources.esm0D HorseCombatMaster.esm0E Colourwheels sixy Female NPCs.esp0F Unofficial Oblivion Patch.esp [Version 3.2.4]10 UOP Vampire Aging & Face Fix.esp [Version 1.0.0]11 DLCShiveringIsles.esp12 Unofficial Shivering Isles Patch.esp [Version 1.4.0]++ MOBS SI.esp [Version 1.2.2a]13 Better Cities .esp14 Francesco's Optional Chance of Stronger Bosses.esp15 Francesco's Optional Chance of Stronger Enemies.esp16 Francesco's Optional Chance of More Enemies.esp17 Francesco's Optional Leveled Guards.esp++ FCOM_Francescos.esp [Version 0.9.9]++ FCOM_FrancescosItemsAddOn.esp [Version 0.9.9]18 FCOM_FrancescosNamedBosses.esp [Version 0.9.9]19 All Natural - Real Lights.esp [Version 0.9.8]1A All Natural.esp [Version 0.9.8]1B All Natural - SI.esp [Version 0.9.8]++ All Natural - EW + NW + AWS.esp [Version 0.9.6]1C Enhanced Water v2.0 HDMI.esp++ dist_trees_x1_5.esp1D RAEVWD New Sheoth.esp [Version 1.5]1E DLCHorseArmor.esp1F DLCHorseArmor - Unofficial Patch.esp [Version 1.0.5]20 DLCOrrery.esp21 DLCOrrery - Unofficial Patch.esp [Version 1.0.3]22 DLCVileLair.esp23 DLCVileLair - Unofficial Patch.esp [Version 1.0.5]24 DLCMehrunesRazor.esp25 DLCMehrunesRazor - Unofficial Patch.esp [Version 1.0.4]26 DLCSpellTomes.esp++ DLCSpellTomes - Unofficial Patch.esp [Version 1.0.1]++ MaleBodyReplacerV4.esp++ ArtifactsFemaleArmor.esp27 XiaNewAmuletsV1.esp28 Armamentium female.esp29 Colourwheels sixy Stock Armor & Clothing Replacer.esp2A Colourwheels sixy SI Armor & Clothing Replacer.esp2B ColourKnights.esp2C DLCThievesDen.esp2D DLCThievesDen - Unofficial Patch.esp [Version 1.0.5]2E DLCThievesDen - Unofficial Patch - SSSB.esp [Version 1.0.4]2F Slof's Oblivion Robe Trader.esp30 Bob's Armory Oblivion.esp31 FCOM_BobsArmory.esp [Version 0.9.9]32 Oblivion WarCry EV.esp33 FCOM_WarCry.esp [Version 0.9.9MB3]34 Oscuro's_Oblivion_Overhaul.esp [Version 1.34]++ OOO_XiaNewAmulets Addon.esp [Version 0.5]++ ArmamentariumLLVendors.esp [Version 1.35]35 ArmamentariumArtifacts.esp [Version 1.35]36 OBSE-Storms & Sound SI.esp37 FCOM_Convergence.esp [Version 0.9.9Mb3]++ FCOM_EntropicOrderRebalance.esp [Version 0.9.9beta2]38 FCOM_RealSwords.esp [Version 0.9.9]39 FCOM_DurabilityAndDamage.esp [Version 0.9.9]++ FCOM_SpawnRatesReduced.esp [Version 0.9.9Mb3]3A Mart's Monster Mod - More Wilderness Life.esp [Version 3.7b3p3]++ Mart's Monster Mod - More Passive Wildlife.esp [Version 3.7b3p3]++ FCOM_SaferRoads.esp [Version 0.9.9]++ FCOM_LessRats.esp [Version 0.9.9]++ FCOM_LessReaversInGates.esp [Version 0.9.9]3B Mart's Monster Mod - Extra Wounding.esp [Version 3.7b3p3]++ Mart's Monster Mod - Looting NPCs & Creatures.esp [Version 3.7b3p3]++ Mart's Monster Mod - No Lanterns.esp [Version 3.7b3p3]++ Mart's Monster Mod - Less Reavers.esp [Version 3.7b3p3]3C Mart's Monster Mod - Dungeons of MMM.esp [Version 3.7b3p3]3D Mart's Monster Mod - Gems & Gem Dust.esp [Version 3.7b3p3]3E Mart's Monster Mod - Hunting & Crafting.esp [Version 3.7b3p3]3F Mart's Monster Mod - Farm Animals.esp [Version 3.7b3p3]++ Mart's Monster Mod - Slof Horses Complete.esp [Version 3.7b3p3]++ Mart's Monster Mod - Diverse Runeskulls Loot G&GD.esp [Version 3.7b3p3]++ FCOM_DiverseGuardUnity.esp [Version 0.9.9]++ FCOM_BobsGuardUnity.esp [Version 0.9.9]++ FCOM_HungersUnitySI.esp [Version 0.9.9]++ FCOM_Archery.esp [Version 0.9.9]++ FCOM_FriendlierFactions.esp [Version 0.9.9]40 FCOM_MoreRandomSpawns.esp [Version 0.9.9]41 FCOM_MoreRandomItems.esp [Version 0.9.9]++ Mart's Monster Mod - Shivering Isles.esp [Version 3.7b3p3]++ ArmamentariumLL4OOO.esp [Version 2.01]++ ArmamentariumLLMagicOOO.esp [Version 1.35]++ Fransfemale.esp++ EVE_StockEquipmentReplacer4FCOM.esp42 CNME v1.4.esp43 CNME Bloodmoon v1.0.esp44 Artifacts.esp++ Artifacts - ArmaCompleteAddon.esp [Version 0.20]45 DLCBattlehornCastle.esp46 DLCBattlehornCastle - Unofficial Patch.esp [Version 1.0.4]47 DLCFrostcrag.esp48 DLCFrostcrag - Unofficial Patch.esp [Version 1.0.4]49 Knights.esp4A Knights - Unofficial Patch.esp [Version 1.0.9]++ EVE_KnightsoftheNine.esp4B SM Plugin Refurbish(Merged).esp [Version 1.21]++ DLC_MOBS.esp++ FCOM_Knights.esp [Version 0.9.9Mb3]++ FCOM_SlofsRobeTrader.esp [Version 0.9.9]4C xuldarkforest.esp [Version 1.0.3]4D xulStendarrValley.esp [Version 1.2.1]4E xulTheHeath.esp4F MMMMWL-TheHeath patch.esp50 XulEntiusGorge.esp51 xulFallenleafEverglade.esp [Version 1.3.1]52 xulColovianHighlands_EV.esp [Version 1.2.1]53 xulChorrolHinterland.esp [Version 1.2.2]54 xulBeachesOfCyrodiilLostCoast.esp [Version 1.6.3]55 xulBravilBarrowfields.esp [Version 1.3.2]56 xulLushWoodlands.esp [Version 1.3]57 xulAncientYews.esp [Version 1.4.2]58 xulAncientRedwoods.esp [Version 1.6]59 xulCloudtopMountains.esp [Version 1.0.3]5A xulArriusCreek.esp [Version 1.1.3]5B xulPatch_AY_AC.esp [Version 1.1]5C xulRollingHills_EV_withoutWheat.esp [Version 1.3.2]5D MMMMWL-RollingHills patch.esp5E xulPantherRiver.esp5F xulRiverEthe.esp [Version 1.0.2]60 xulBrenaRiverRavine.esp [Version 1.0.2]61 xulImperialIsle.esp [Version 1.6.3]62 xulBlackwoodForest.esp63 xulCheydinhalFalls.esp [Version 1.0.1]64 xulAspenWood.esp [Version 1.0.1]65 RingOfWings_Wingless.esp66 Enhanced Vegetation [150%].esp67 Deadly Reflex 5 - Timed Block with no damage or durability changes.esp68 DeadlyReflex 5 - Combat Moves.esp++ Slof's Oblivion Better Beasts.esp69 xeoex.esp6A Morroblivion eye fixes.esp6B Better Cities Full.esp6C Better Cities - Unique Landscape Barrowfields.esp6D Better Cities - Unique Landscape Chorrol Hinterland.esp6E Better Cities - Unique Landscape Cheydinhal Falls.esp6F Better Cities - No LEYAWIIN Flooding.esp70 Better Imperial City.esp71 Better Imperial City FPS Patch.esp72 Better Cities Full FPS Patch.esp73 QQuix - Rock, rock, rock your ship - V3.esp++ CoreRandmonClothing4Npcs.esp** All Natural - Indoor Weather Filter For Mods.esp [Version 0.9.8]74 Knight of Skeleton.esp75 meat crusher.esp76 Bashed Patch, 0.esp77 FormID Finder4.esp78 Streamline 3.1.esp79 RedDelPCB.esp