If references are fine, then check their base STAT (SCOL and ACTI) records. LOD mesh name depends on the full mesh name, if any mod changes them, FNVLODGen won't fine corresponding LOD meshes.
Like I said you need to do some investigation with your load order, because it works for me. Still want to hear reports from others too regarding those places. If it'll work for them, then something is definitely wrong in your setup.
Nothing is changing most of the area, there is one house added across the street from the schoolhouse, and a copy of the Goodsprings General store is placed which is used as Frankie's Guns and Ammo. None of the meshes are altered that I can find.
AWOP uses vanilla assets entirely, impossible for it to be the cause.
I don't think Chuck has altered any of those assets with Interiors but he'll have to chime in on that.
I'll check closer into Afterschool Special, Russell and New Bison Steve as they are the only other NV mods I'm using at this time.
Rise fixed the sign one, and the wrong texture for the rocks was caused by NMC's pack.
I still need to look for the other ones, I will make a clean TTW install and check the LOD gen with only the esm's for the NV wasteland.
New Bison and Afterschool special don't alter any models, their BSA's are almost entirely just audio and lip files.
Maybe some ini settings also affecting LOD if you changed them?
Anyway, please pack generated LOD for WastelandNV worldspace (including atlas) and upload, I want to check what could be wrong there.
File, thanks go to Roy for making half of it 
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Thx Risewild, looking hot! Furs off 
About monorail issue, it is actually not FNVLODGen's fault. The mesh for that monorail curve meshes\architecture\urban\monorail\nv_mrcurvedmg01_lod.nif has rotation set in main BSFadeNode
http://i.imgur.com/QxrlvTL.png
FNVLODGen respects those settings and adjust mesh when generating LOD, by GECK and Creation Kit ignore them. Fortunately lodgen can ignore translation/rotation on particular meshes from provided list, and I'll be including such meshes into it. For now just set rotation/translation to 0 on those meshes in NifScope and report them here. I guess other "deformed" lod meshes you've seen has probably the same issue in meshes.
Don't know about fort walls, they are fine in vanilla game when I generate LOD for Freeside. Will need to install Freeside Open to find out what could be wrong there.
Downloaded Freeside Open, after checking the archive I already knew what's wrong even without installing it. There is a new mesh for fort meshes\rzw\freesideopen\oldmormonfort2.nif and it requires the corresponding _lod.nif mesh for LOD which is missing. So you either need to create a new lod mesh for it, or get the vanilla one
meshes\architecture\strip\oldmormonfort_lod.nif
and copy it as
meshes\rzw\freesideopen\oldmormonfort2_lod.nif
However vanilla lod mesh contains opened gates which were removed in rzw's mesh, so there will be gates in lod but no gates when up close.
I think this was the last reported issue for New Vegas. Time to move on to TTW FO3 worldspaces and DLCs and hunt for bugs there. So far the common issues are:
1) Black rectangles - no alpha in diffuse LOD texture
2) "Deformed" meshes - translation/rotation set in lod mesh itself
3) Missing meshes - lod meshes are actually missing, could also be the above case with large translation value that moves lod out of sight (under the ground for example)
4) "wrong" texture in lod, well I guess it is just a very low quality of lod textures in general
Anything else?
Thanks Zilav! I just woke up and now I don't have to go look. :D
:EDIT:
All NV LOD looking good.
Could you make it report the lod mesh that is missing textures? I don't know what mesh is missing textures so I how the heck am I supposed to find the correct ones. :)
Some of the meshes don't even line up with the high poly ones at all, the overpass roads are one and the monorails are another. Same goes for the large satellite dishes.
There is a lot of pieces which don't have any lod mesh, some of the road pieces and rocks, bunker entrances. The Freeside sign is way worse quality than the other strip/freeside signs that actually have lights on them. Doors don't have lod meshes either from what I can see.
I am hoping someone steps up and starts a high quality LOD pack.
