I have a similar problem. Parts of my avatar become invisible (parts of arms, legs and neck). I've tried loading the test avatar, clearing the cache, different viewers, rebaking textures.
I think the problem dates from a nasty RLV trap I fell in (moral: don't lean on lampposts in suspect areas!). It changed my head to the same one visible in the first post on this thread. I think there are some nasty virus-like alpha masks that have now been planted somewhere in my inventory and their file names hidden.
At one point, when I did a Ctrl-Alt-T I could see the teeth of the replaced head (see the first post picture) on the missing part of one leg.
I think someone created this problem deliberately.
Is there such a thing as an "inventory cleaner" that could find these alpha masks and delete them?
C