Hmmm. Post you're load order if u can pls. Should be something like this :
[X] Fallout3.esm
[X] PointLookout.esm
[X] Anchorage.esm
[X] ThePitt.esm
[X] BrokenSteel.esm
[X] Zeta.esm
[X] CALIBR.esm
[X] CRAFT.esm
[X] FO3 Wanderers Edition - Main File.esm
[X] FO3 Wanderers Edition - Main File.esp
[X] FO3 Wanderers Edition - Followers Enhanced.esp
[X] FO3 Wanderers Edition - DLC Anchorage.esp
[X] FO3 Wanderers Edition - DLC The Pitt.esp
[X] FO3 Wanderers Edition - DLC Broken Steel.esp
[X] FO3 Wanderers Edition - Followers Enhanced (BrokenSteel).esp
[X] FO3 Wanderers Edition - DLC Point Lookout.esp
[X] FO3 Wanderers Edition - DLC Mothership Zeta.esp
From the zip file:
The esm and esp go to the ".../Fallout3/Data" folder
The textures, meshes, souds folders go to the same ".../Fallout3/Data" folder thus creating ".../Fallout3/Data/Textures", and so on.
Don't forget to invalidate older files through Falloyt Mod Manager.
I got it installed here on my GOTY edition - version is FWE 5.02 and its all fine.
Hope this helps?