Ran into an unusual problem which i finally resolved. I thought it might
be of interest to others. The problem occurs when you include/input
files that have spaces in them and then you try to process the generated
tex file seperately. When Lyx generates the tex for the master file it
generates somethihg like:
\include{\string"Filename with spaces"\string}
But when you process this with latex/pdflatex it generates an aux file
containing
\@input{"Filename.aux}
which of course causes no end of confusion to both latex and bibtex.
Removing the spaces fixes the problem
