I am having identical problem. None of these work: Rebaking; Clearing cache; Rebooting PC & modem; Choosing default avatar.
Oddly, if I choose editing appearance, such as skin, etc all the menu textures such as for pigments (light & dark) even with a default avatar, are psychedellic squares. I am using the latest, official SL viewer on Windows Vista on a Dell M6300 workstation laptop.
All I can see of myself as the default avatar Male Explorer are prim objects: hat, collar, belt, whip and boots. Other than that I can see my eyeballs, but they are pixelated. Doing a texture rebake made all other parts invisible. Prior to the rebake the now-invisible parts were psychedelic half-transparent. Sometimes those parts of me look inside out or banded. Sometimes they look like a Star Trek transported person stuck half-way.
I've been in SL since 2008 but this issue is getting to be frustrating enough that I almost want to just quit. If not for my SL GF, I would have already.