Latex installation or workspace configuration breaking \begin{enumerate}

Task Description: I am writing my thesis with latex in vscode. Sometimes I write using my desktop PC and other times using my laptop when I am travelling. I have setup git version control for this reason and for obvious backup reasons.

Issue Description: I tried making a list using the itemize function, which caused several issues when building the project only in my desktop. Things work fine when I am working on my laptop. In addition, I am getting warnings regarding undefined citations, even though the entries are in the .bib file and the built pdf file shows the correct citation number.

Debug message: The troubling code and accompanying error messages are shown below.

When I comment out this part of the code, I get the error message

I am attaching main.tex code to show the preamble.

\documentclass[11pt]{report}
\usepackage[
  dissertation
 ,final
 ,raggedbottom
%,tocbold        % uncomment to enable bold chapter titles in the ToC
                 %
                 % the style guidelines state that page numbers in the
                 % ToC should not be bold, but leave it up to the author
                 % and specific department guidelines as to how the
                 % chapter (or other section) titles should be typeset.
]{USCthesis}

% guidelines for manuscript formatting: https://graduateschool.usc.edu/wp-content/uploads/2020/11/Manuscript_Formatting_and_Documentation_Styles.pdf

%% our customizations %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% \usepackage[export]{adjustbox} % for frame option in \includegraphics
\usepackage{amssymb} % for mathematical symbols
% \usepackage{array} % for advanced table formatting
\usepackage[utf8]{inputenc} % for input encoding
\usepackage[english]{babel} % for language support
\usepackage[backend=biber, doi=true, hyperref=true, maxbibnames=199, sortlocale=en_US, style=numeric]{biblatex} % for bibliography management
% \usepackage{booktabs} % for professional-looking tables
\usepackage{color, colortbl} % for color support
\usepackage{csquotes} % for advanced quotation handling
\usepackage{efbox} % for framed boxes
\usepackage{amsmath} % for advanced mathematical typesetting
\usepackage{enumitem} % for customizing lists
\usepackage[shortcuts]{extdash} % for hyphenation of words with dashes
\usepackage[tt=false]{libertine} % for a specific font
\usepackage[T1]{fontenc} % for font encoding
\usepackage[symbol]{footmisc} % for customizing footnotes
\usepackage[showframe=false, pass=true]{geometry} % for page layout customization
\usepackage{graphicx} % for including graphics
\usepackage{pgfplots} % for creating plots
\usepackage{hyphenat} % for hyphenation control
\usepackage{amsfonts} % for mathematical fonts
\usepackage{braket} % for Dirac notation
% \usepackage{parnotes} % for footnotes in tables
\usepackage{pdflscape} % for landscape pages
\usepackage{pifont} % for special symbols
\usepackage{ragged2e} % for advanced text alignment
\usepackage{seqsplit} % for splitting long sequences of characters
\usepackage{enumitem}
\usepackage{siunitx} % for typesetting SI units
\usepackage{subcaption} % for subfigures and subtables
% \usepackage{tabularx} % for advanced table formatting
\usepackage{xcolor} % for color support
\usepackage{xspace} % for intelligent spacing
\usepackage{url} % for typesetting URLs
\usepackage{hyperref} % for hyperlinks
\usepackage[utf8]{inputenc}
% \usepackage[
%   breaklinks    = true,
%   colorlinks    = true,
%   hypertexnames = True,
%   pdfpagelabels = false,
%   citecolor     = {blue!80!black},
%   linkcolor     = {blue!80!black},
%   urlcolor      = {blue!80!black},
% ]{hyperref} % load hyperref as the last package

% pkg: biblatex
\setlength\bibitemsep{0.5\baselineskip}                 % add a line between entries
\AtEveryBibitem{\iffieldundef{doi}{}{\clearfield{url}}} % if DOI, hide URL

\addbibresource{thesis.bib}

% pkg: siunitx
% some guidelines https://physics.nist.gov/cuu/Units/checklist.html
\sisetup{
  tight-spacing  = true
  ,detect-family = true
  ,detect-mode   = true
  ,binary-units  = true    % support for MB, GB, etc.
  ,range-units   = single  % "3% to 5%" -> "3 to 5%"
  ,range-phrase  = --      % "3 to 5%"  -> "3--5%"
}

% pkg: babel, hyperref
\addto\extrasenglish{%
  \renewcommand{\chapterautorefname}{Chapter}
  \renewcommand{\sectionautorefname}{Section}
  \renewcommand{\subsectionautorefname}{Section}
  \renewcommand{\subsubsectionautorefname}{Section}
}

% pkg: url
\renewcommand{\UrlFont}{\footnotesize\tt}

% our custom commands
\renewcommand{\ttdefault}{cmtt} % use computer modern for teletype

%%% draft mode / toggle commands %%%
\usepackage{etoolbox}
\newtoggle{draft}
\settoggle{draft}{true} % change toggle for draft or final versions

\iftoggle{draft}{
  % if 'draft' toggle is true
  \overfullrule=10pt                       % highlight overfull hboxes
}{
  % if 'draft' toggle is false
  \PassOptionsToPackage{final}{showlabels} % hide labels on figures, etc
}

% if you're including existing papers into your thesis, it helps to put
% content behind a toggle (or conditional) so you only have to maintain
% and keep consistency on one copy. see "introduction.tex".
\newtoggle{thesis}
\settoggle{thesis}{true}

% \usepackage[inline]{showlabels} % only used for debugging
% \renewcommand{\showlabelfont}{\sffamily \color{blue}}
% \renewcommand{\showlabelsetlabel}[1]{\efbox{\showlabelfont #1}}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%% front matter %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{document}

% title should be all caps
\title{HARNESSING CLASSICAL CONTROL FOR GENERATING ARBITRARY QUANTUM DYNAMICS IN SUPERCONDUCTING QUBITS}
% ALT TITLE: DEVELOPMENT OF NOVEL STOCHASTIC AND HAMILTONIAN CONTROL TECHNIQUES FOR SUPERCONDUCTING QUBITS 

% use your full name!
% https://cs.stanford.edu/~knuth/news19.html
% "Let's celebrate everybody's full names"
\author{Evangelos Vlachos}
 
% major should be all caps
\majorfield{PHYSICS}

% date should be May, August, or December (when degrees are conferred)
\submitdate{August 2024}

%%% preface %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{preface}
  % \prefacesection{Dedication}
  \input{chapters/dedication.tex}

  % \prefacesection{Acknowledgements}
  \input{chapters/acknowledgements.tex}

  {
  \hypersetup{hidelinks} % color all links black in the preface
  \tableofcontents
  \listoftables
  \listoffigures
  }

  % \prefacesection{Abstract}
  \input{chapters/abstract.tex}

\end{preface}

%%% introduction %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% \input{chapters/introduction.tex}

% \input{chapters/light_matter_interaction.tex}

\input{chapters/noise-sources.tex}

\input{chapters/open-quantum-systems.tex}
  
\input{chapters/hardware.tex}

\input{chapters/master-equation-paper.tex}

\input{chapters/coherence-stabilization.tex}


%%% conclusions %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\input{chapters/conclusions.tex}

%%% bibliography %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
%  \printbibliography in biblatex is great, but doesn't allow for the
%  greatest customization, so we'll use the package biblatex + biber
%  backend to meet some requirements:
%
%  * bibliography should be an un-numbered chapter, and still have a
%    pdfbookmark and a line in the table of contents
%
%  * bibliography contents should be singlespace, and optionally a smaller
%    font
%
%  * first line of this "chapter" should be in the same spot as the first
%    line of preface sections (e.g., acknowledgement)
%
%  * we use \raggedright so things like URLs and DOIs aren't stretched out.
%
\clearpage
\chapter*{Bibliography}
\addcontentsline{toc}{chapter}{Bibliography}

\begin{singlespace}
  % increase penalty such that we don't break entries over pages
  % source: https://tex.stackexchange.com/a/43275
  \patchcmd{\bibsetup}{\interlinepenalty=5000}{\interlinepenalty=10000}{}{}

  % reduce spacing between each bibentry
  \setlength\bibitemsep{0.9\baselineskip}

  % don't justify-align entries: this prevents stretching out each line
  \raggedright
  \printbibliography[heading = none]
\end{singlespace}

\end{document}