This sounds similar to a problem I had with my floors a while back.
I had two thumbnails each for several custom floors, and when I deleted one of the copies ingame, the one that was left would show up as just the plywood underflooring when I placed it.
It took me forever to find that I had a duplicate copy of my "Floors" subfolder hiding in my "Saved Sims" folder (long story having to do with a child of mine burning copies of my downloads onto cd's for me
) Anyway, getting rid of the duplicates in the "saved sims" folder fixed the problem for me, so I'm wondering if you might also have duplicate files hiding in some strange place in your game? Just a thought...