lilypond-book rotates some elements

[Dan Bowtell]

When I started creating my lilypond book all the music excerpts appeared 
perfectly normal. Then lilypond decided it wanted to change that and make me 
miserable. Now all beams, stems and some other elements are rotated 90 
degrees. I've tried taking the book back to its state before, including 
deleting all the generated files but i can't get everything back the right 
way round. Has anyone else experienced this?

Link to screengrab of problem: 
http://bowtell.demon.co.uk/~vrih/images/lily.png
Sourcefile: http://bowtell.demon.co.uk/~vrih/major_scale.tex

Thanks in advance for any advice you can give me.

Dan