(Screenshots provided by hicham)
http://img21.imageshack.us/i/amnesiascreenshot000.jpg/
http://img168.imageshack.us/i/amnesiascreenshot002.jpg/
The info I got from the lead dev is it is most likely a texture coordinate issue in the Mesa drivers. Basically the game renders things offscreen to a backbuffer/intermediate texture using the FBO extensions in OpenGL. Then that single texture is rendered to the screen. then later draws all of the transparent items on-top (ie.. the candles and flame, etc..)
So what you are seeing is most likely caused by mesa GL somewhere reversing the texture coordinates accidentally. I would start there in your bug reports with Mesa