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Hi both, thanks for the quick reply and welcome! I had already tried running with both -inc and -merge options. Have just tried moving the chapter tex files up to the main directory and that fixed my problem! Thanks again

I have been unable to run texcount ( texcount ) on main.tex in Masters/Doctoral Thesis (version 2.4, from http://www.LaTeXTemplates.com ) and have it count all included files.

The include block looks like

%\include{Chapters/Chapter1}
\include{Chapters/1intro}
\include{Chapters/2theory}
\include ...