Now I'm certain this is an issue relating to a mod, though I'm not entirely sure, but if anything it's NMC's texture pack, which I finally got working after realizing Archive Invalidation was in fact not Invalidated. Now, it seems, that there are giant blocks of missing geometry, whether that be walls in some of the metro tunnels or the land around the Chrysus building, which itself is also covered, for some odd reason, in the LOD texture as opposed to the close up texture which it should have. The giant blocks of missing geometry also seem to drop into the game's water level if I try to walk on them, which is, in and of itself odd.

Here's a screenshot from below the missing land, looking up. If you want, I'll get one looking at the missing land from the top down.

http://i2.photobucket.com/albums/y35/GTAKING/problemo.png

Here's my load order as dictated by BOSS, though I doubt it'll help in this situation. Any ideas?

Anchorage.esmThePitt.esmBrokenSteel.esmPointLookout.esmZeta.esmProject Beauty.esm  . Bashed Patch tag suggestion:  {{BASH:NpcFaces,Hair,Eyes,Voice-M,Voice-F,Body-M,Body-F,R.Teeth,R.Mouth}}Hairday.esmDestruction.esm  . Bashed Patch tag suggestion:  {{BASH:Destructable,Script}}CALIBR.esmxCALIBR.esm  . Bashed Patch tag suggestion:  {{BASH:Names,Graphics,Stats}}Mart's Mutant Mod.esm  . Bashed Patch tag suggestion:  {{BASH:Invent,Relations,Delev}}Enhanced Weather - Rain and Snow.esmRTS.esm  . Conflicts with: ArefuExpandedByAzar.esm  . Conflicts with: 1PipboyPDA.espProject Beauty- Broken Steel.esp  . Bashed Patch tag suggestion:  {{BASH:NpcFaces,NoMerge}} and deactivate.Project Beauty- Point Lookout.esp  . Bashed Patch tag suggestion:  {{BASH:NpcFaces,NoMerge}} and deactivate.DarNifiedUIF3.espCALIBRxMerchant.esp  . Requires:  CALIBR.ESMGalaxyNewsRadio100[M].esp  . Conflicts with:  GalaxyNewsRadioXXX[M].espGalaxyNewsRadio80[M].esp  . Conflicts with:  GalaxyNewsRadioXXX[M].espGalaxyNewsRadio60[M].esp  . Conflicts with:  GalaxyNewsRadioXXX[M].espGalaxyNewsRadio40[M].esp  . Conflicts with:  GalaxyNewsRadioXXX[M].espGalaxyNewsRadio20[M].esp  . Conflicts with:  GalaxyNewsRadioXXX[M].espMarkB50K_Wasteland_Patrols.esp  . Requires: Anchorage.ESM, ThePitt.ESM, BrokenSteel.ESM, PointLookout.esmDestruction - Main.esp  . Bashed Patch tag suggestion:  {{BASH:Destructable,Script,Graphics}}Destruction - Main - Statics.espDestruction - DLC.esp  . Bashed Patch tag suggestion:  {{BASH:Destructable,Script}}Destruction - DLC - Statics.espFOOK2 - [DESTRUCTION] Main.esp  . Bashed Patch tag suggestion:  {{BASH:Destructable,Script}}  . Requires:  FOOK2 - Main.ESMFOOK2 - [DESTRUCTION] Main - Statics.esp  . Requires:  FOOK2 - Main.ESMFOOK2 - [DESTRUCTION] DIK.esp  . Bashed Patch tag suggestion:  {{BASH:Destructable,Script}}  . Requires:  Anchorage.ESM, ThePitt.ESM, BrokenSteel.ESM, PointLookout.esm, CALIBR.ESM, and FOOK2 - Main.ESMFOOK2 - [DESTRUCTION] DIK - Statics.esp  . Requires:  Anchorage.ESM, ThePitt.ESM, BrokenSteel.ESM, PointLookout.esm, CALIBR.ESM, and FOOK2 - Main.ESMFOOK2 - [DESTRUCTION] Mothership Zeta.esp  . Bashed Patch tag suggestion:  {{BASH:Destructable,Script}}  . Requires:  FOOK2 - Main.ESM and Zeta.ESMFOOK2 - [DESTRUCTION] Mothership Zeta - Statics.esp  . Requires:  FOOK2 - Main.ESM and Zeta.ESMWeaponModKits.esp  . Bashed Patch tag suggestion:  {{BASH:Deflst,Reflst}}WeaponModKits - OperationAnchorage.esp  . Requires: Anchorage.ESMWeaponModKits - ThePitt.esp  . Requires: ThePitt.ESMWeaponModKits - BrokenSteel.esp  . Requires: BrokenSteel.ESMWeaponModKits - PointLookout.esp  . Requires: PointLookout.ESMWeaponModKits - Zeta.esp  . Requires: Zeta.ESM3EFdrg.espsunglassescollection.espxCALIBRmunitions.espxCALIBRmunitions_FOSEnhancements.espEVE.esp  . Bashed Patch tag suggestion:  {{BASH:Graphics,Sound}}EVE Operation Anchorage.esp  . Requires:  Anchorage.ESMEVE Operation Anchorage.esp  . Bashed Patch tag suggestion:  {{BASH:Graphics,Sound}}  . Requires: Anchorage.ESMMart's Mutant Mod.esp  . Bashed Patch tag suggestion:  {{BASH:Delev}}  . Requires: Mart's Mutant Mod.esmMart's Mutant Mod - Project Beauty.esp  . Bashed Patch tag suggestion:  {{BASH:NpcFaces,Hair,Eyes,Voice-M,Voice-F,Body-M,Body-F,R.Teeth,R.Mouth}}Mart's Mutant Mod - DLC Anchorage.esp  . Requires:  Anchorage.ESMMart's Mutant Mod - DLC The Pitt.esp  . Bashed Patch tag suggestion:  {{BASH:Delev}}  . Requires:  ThePitt.ESMMart's Mutant Mod - DLC Broken Steel.esp  . Bashed Patch tag suggestion:  {{BASH:Delev,Relev}}  . Requires:  BrokenSteel.ESMMart's Mutant Mod - DLC Point Lookout.esp  . Bashed Patch tag suggestion:  {{BASH:Delev,Relev}}  . Requires:  PointLookout.ESMMart's Mutant Mod - DLC Zeta.esp  . Requires:  Zeta.ESMMart's Mutant Mod - Feral Ghoul Rampage.esp  . Bashed Patch tag suggestion:  {{BASH:Relev}}Mart's Mutant Mod - Hunting & Looting.espMart's Mutant Mod - Natural Selection.esp  . Bashed Patch tag suggestion:  {{BASH:Relations,NoMerge}} and deactivate.Mart's Mutant Mod - Tougher Traders.espRTSpatch_RVW.espEnhanced Weather - Rain and Snow in Fallout.espEnhanced Weather - Radioactive Rain and Snow Plugin.espEnhanced Weather - Weather Sounds in Interiors.espEnhanced Weather - Sneak Bonus during Storms.espDestruction - CP - Fellout.espDestruction - CP - Fellout.espxCALIBR_override.esp  . Bashed Patch tag suggestion:  {{BASH:Names,Graphics,Stats}}  . Requires: CALIBR.esm, xCALIBR.esm-----------------------------------------------------------------Unrecognised mod files:                                          Reorder these by hand using your favourite mod ordering utility. -----------------------------------------------------------------Unknown mod file: Abbreviated Effects.esmUnknown mod file: asas.espUnknown mod file: Partical Magnum.espUnknown mod file: MM6U.espUnknown mod file: ColtAnaconda.espUnknown mod file: TUPAM.espUnknown mod file: TUPAM - Anchorage Addon.espUnknown mod file: TUPAM - Broken Steel Addon.espUnknown mod file: TUPAM - The Pitt Addon.espUnknown mod file: TUPAM - Uninstaller.espUnknown mod file: TUPAM+FOOK - Anchorage Addon.espUnknown mod file: TUPAM+FOOK - Broken Steel Addon.espUnknown mod file: TUPAM+FOOK - The Pitt Addon.espUnknown mod file: TUPAM+FOOK.espUnknown mod file: helm nv.espUnknown mod file: japanese_armor_set.espUnknown mod file: lod clipping.espUnknown mod file: MaxLevel100.espUnknown mod file: AdvancedReconGear.espUnknown mod file: lod clipping fix.espUnknown mod file: Moonlight.espUnknown mod file: Starlight.espUnknown mod file: ArmoredVault101SuitRepairmod3.esp

It's Destruction.

Aww, well appreciated, thanks. I imagine it had something to do with the new textures and the Destruction ESP not matching up properly?

It's a common engine bug, restart your game and it should go away.