I'm getting the notorious flickering/wrong textures for some guns, and also the fast-travel motorcycle added by FWE. The texture problems are affecting weapons from several different mods. I have turned on archiveinvalidation in FOMM, as well as checking the .ini files manually. Deactivating and reactivating it doesn't seem to help either.

Fallout3.esmAnchorage.esmThePitt.esmBrokenSteel.esmPointLookout.esmZeta.esmCRAFT.esmCALIBR.esmAdvanced Recon Tech.esmEVE.esmApocalypse Armory.esmFO3 Wanderers Edition - Main File.esmDarNifiedUIF3.espPLweightadjust.espApocalypse Armory - CALIBR.espApocalypse Armory - DLC Enhancements.espFO3 Wanderers Edition - Main File.espFO3 Wanderers Edition - DLC Anchorage.espFO3 Wanderers Edition - DLC The Pitt.espFO3 Wanderers Edition - DLC Broken Steel.espFO3 Wanderers Edition - DLC Point Lookout.espFO3 Wanderers Edition - DLC Mothership Zeta.espFO3 Wanderers Edition - Alternate Travel.espFO3 Wanderers Edition - Followers Enhanced (BrokenSteel).espFO3 Wanderers Edition - Optional Restore Tracers (automatics only).espRefurbishes [ALL].espRefurbish [OA] - FWE.espWeaponModKits.espWeaponModKits - FWE Master Release.espWeaponModKits - OperationAnchorage.espWeaponModKits - ThePitt.espWeaponModKits - BrokenSteel.espWeaponModKits - PointLookout.espWeaponModKits - Zeta.espApocalypse Armory + WMK.espAdvanced Recon Gear.espAdvanced Recon Armor.espBABEreconarmor.espJillBSAA.espInvisArcadeIndustries_SweetSneak.espEVE.espEVE Operation Anchorage.espEVE - FWE Master Release.espEVE - FWE Master Release (Follower Enhanced).espEVE - FWE Master Release (pulse fix).espEVE Anchorage - FWE DLC Anchorage.espEVE - FWE with WeaponModKits.espApocalypse Armory + EVE.espMentatsMod.espQApplebysOutfit.espChineseHeavyArmor.espmergedpatch.espOMFG.espmergedpatch1.espTotal active plugins: 54Total plugins: 59

Was the flickering white? I'm not sure what exactly went wrong with your guns but, every now and then my enviornment flickers into a white outline of what should be Megaton. Reply with the exact details of what happened and also post updates of what you hav tried and the outcomes. If you do that, I might just be able to help you fix your problem.

The only thing I see that jumps out at me is...

mergedpatch.esp

mergedpatch1.esp

Two merged patches? You should only need one, try removing both and then build a fresh new merged patch and see if that helps.

Oof, I must have been pretty tired to let the old merged patch slip past me. Made a new one, but no change so far, even when starting a new game. Here are some pics, they will describe the problem better than I can.

http://imageshack.us/photo/my-images/845/gunk.jpg/
http://imageshack.us/photo/my-images/191/cycleu.jpg/

The gun is from Apocalypse Armory, the motorcycle from FWE. I have also found a gun from OMFG.esp with the same problem.

There's a great utility called FormID Finder.esp in Oblivion that shows what mesh and texture a model is using. Is there anything like that for Fallout? It would be nice to make sure the models are pointing towards the right textures (and that they are installed).

Just be to sure, bInvalidateOlderFiles is set to 1 in the Fallout.ini? ArchiveInvalidationInvalidated!.bsa is the first .bsa under SArchiveList in the .ini?
Try removing the ArchiveInvalidationInvalidated!.bsa from your Data folder and reactivating Archive Invalidation through FOMM so you know a new .bsa is created.

With the motorcycle's mis-matched textures it looks like the TextureList isn't being used properly. You could try a MasterUpdate with FO3Edit and see if that helps.

I tried this, no luck. Looking at Fallout.ini did turn up something strange though:

[GeneralWarnings]SGeneralMasterMismatchWarning=One or more plugins could not find the correct versions of the master files they depend on. Errors may occur during load or game play. Check the "Warnings.txt" file for more information.SMasterMismatchWarning=One of the files that "%s" is dependent on has changed since the last save.This may result in errors. Saving again will clear this messagebut not necessarily fix any errors.[Archive]SMasterMiscArchiveFileName=Fallout - Misc.bsaSMasterVoicesArchiveFileName1=Fallout - Voices.bsaSMasterVoicesArchiveFileName2=Fallout - MenuVoices.bsaSMasterSoundsArchiveFileName=Fallout - Sound.bsaSMasterTexturesArchiveFileName1=Fallout - Textures.bsaSMasterMeshesArchiveFileName=Fallout - Meshes.bsaSInvalidationFile=iRetainFilenameOffsetTable=1iRetainFilenameStringTable=1iRetainDirectoryStringTable=1bCheckRuntimeCollisions=0bInvalidateOlderFiles=1bUseArchives=1SArchiveList=ArchiveInvalidationInvalidated!.bsa, Fallout - Textures.bsa, Fallout - Meshes.bsa, Fallout - Voices.bsa, Fallout - Sound.bsa, Fallout - MenuVoices.bsa, Fallout - Misc.bsa]

The plugins not being able to find their masters doesn't sound right, and I'm also a little puzzled as to why "SInvalidationFile=" doesn't have a variable.

I have done a MasterUpdate after each change, but I don't think I have tried running FO3 without it. I'll reinstall my FOMOD packages this evening and see if that helps. Thanks for your suggestions!
Edit: I couldn't find this "warnings.txt" file, even after running search on the entire HDD. Yarrr