If you get an error like this, or any error while latex'ing the thesis files when you're just beginning with your thesis, make sure that you're not trying to \include files that don't exist. If you use `all' and the main.tex file tries to include files that don't exist, then it will mess up with that error, and corrupt the .aux files. To fix this,
a) comment out the \include lines that correspond to files that you haven't created files for yet by changing them from
for all the files that you include. `touch' will create the files if they don't exist.
Then, delete all the bonus extra files
And try it again. It should work.