Yes, you are both right. The beta version of better bodies put the texture files in 'Data files/Textures' but the newer release put them into 'Data Files/Textures/BB'
To get TESXMC to work, move the textures from 'Data Files/Texture/BB' to 'Data Files/Textures' then run TESXMC. When it's done, move the textures back again.
This is quite a major bug and I am sorry. When I tested it, a had no mods that used sub-folders in the textures folder, so it dosn't work.
This is true not only for Better Bodies' but also 'Better Heads' and any other mod that uses sub folders. Hope this helps.