Keep Coding

I am using auctex with aquamacs and I have added the following lines at the ned of my latex file:
%% Local Variables:
%% mode: latex
%% TeX-master: "book"
%% End:
However, when I latex the current file it processes the whole masterfile and not just the header. I have checked TexHeaderEnd
TeX-header-end is a variable defined in `tex.el'.
Its value is "^[^%
]*\\\\begin *{document}"
not sure why there is a newline in the middle?
Also I have used the same setup in the past and it also doesn't work with files for which it worked in the past.
I have also installed a new version of aquamacs (does this install a new version of auctex?).
Any help appreciated.

Found the answer myself. In the past C-c C-c would just apply the command to the buffer but this has changed and C-C C-C applies the command to the masterfile. If you want to typeset the buffer you have to type C-c C-b.