Sounds similar to the problems I was having last night.

In the UV editor (windows -> rendering thingy -> uv editor)
have a look at what the current UVmap is (something like image -> the bottom option, in the menus) that you are using. I had the UV's of my characters head in the default UVmap and also a second one so it was going screwy. To get round it I copied my nicely laid out UV's to the default UVmap and deleted the extra ones.

Might not make too much sense but I get the feeling something like that has happened...