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Thanks for your help Stefan. You too Johannes.

Cheers!

Well, I didn't have time to read a tutorial, so I just used this workaround:
On the main.tex file, I typed this:

\mainmatter % Begin numeric (1,2,3...) page numbering

\pagestyle{thesis} % Return the page headers back to the "thesis" style

\include{Chapters/Chapter1}
\include{Chapters/Chapter2 ...

Well, this configuration came with with Vel's Masters/Doctoral Thesis template. I figured it had something to do with chapter/figure/table numbering. Plus it worked fine while I was writing my thesis, until the error kind of came out of nowhere.
My problem right now is that Chapter3's numbering just ...

So, the commands section in each of my chapter files looks like this:

Chapter 1:

\newcommand{\keyword}[1]{\textbf{#1}}
\newcommand{\tabhead}[1]{\textbf{#1}}
\newcommand{\code}[1]{\texttt{#1}}
\newcommand{\file}[1]{\texttt{\bfseries#1}}
\newcommand{\option}[1]{\texttt{\itshape#1}}
Chapter 2 ...