fancylabel not incrementing counter if table is include with ltxtable

Question

I'm using ltxtable to use flexible width, tabularx, X columns in a long-table. I'm also using the chemschemex/fancylabel package to give me sweet sweet automatic numbering of my chemical structures.

However, if I include a table containing \fancylabel[<family>]{label} commands via the \LTXtable{<width>}{<file>} method the counter for the fancylabels doesn't increment. And so, all labels end up with the same number.

Including the same table, just with the X columns substituted for l columns, directly in the document or via an \input{} command gives the correct sequential numbering.

None of the inclusion method effects the numbering throughout the document, only that of the table. The table also recognises previously numbered structures and assigns the correct number to them, but then for the next structure fails to change the counter.

\documentclass[a4paper]{article}
\usepackage{graphicx}
\usepackage{siunitx}
\usepackage{chemmacros}
  \chemsetup{modules = nomenclature}

\let\etoolboxforlistloop\forlistloop % save the good meaning of \forlistloop
\usepackage{chemschemex}
\let\forlistloop\etoolboxforlistloop % restore the good meaning of \forlistloop

\usepackage{threeparttable}
\usepackage{threeparttablex}
\usepackage{longtable}
\usepackage{tabularx}
\usepackage{ltxtable}
\usepackage{collcell}
\usepackage{afterpage}

\begin{filecontents}{table.tex}
  \begin{ThreePartTable}
    \begin{TableNotes}
      \item [a] A note.
    \end{TableNotes}
    \begin{longtable}[c]{%
      @{}%
      >{\bfseries}l<{}%
      >{\collectcell\iupac}X<{\endcollectcell}% This is the column with the tabularx `X` column when using ltxtable
      S%
      @{}%
    }
      \caption{Caption!}\\
      \multicolumn{2}{@{}l}{\textbf{Molecule}} & {\pKa}\\
      \endfirsthead

      \insertTableNotes
      \endlastfoot

      \multicolumn{2}{@{}l}{\emph{Pyridines}}                             \\
      \fancylabel[CSX]{pyr}      &  pyridine            &  5.23           \\
      \fancylabel[CSX]{2me-pyr}  &  2-methylpyridine    &  5.97           \\
      \multicolumn{2}{@{}l}{\emph{Diazines}}                              \\
      \fancylabel[CSX]{pdz}      &  pyridazine          &  2.24\tnote{a}  \\
      \multicolumn{2}{@{}l}{\emph{Phenols}}                               \\
      \fancylabel[CSX]{phe}      &  phenol              &  9.99           \\
      \fancylabel[CSX]{23me-phe} &  2,3-dimethylphenol  &  10.50          \\
    \end{longtable}
  \end{ThreePartTable}
\end{filecontents}

\begin{document}
This is a label: \fancylabel[CSX]{phe}\\
This is an image using chemschemex: \struct[text]{pyr}\\
This is the referenced number for pyridine: \structref{pyr}\\

% No sweet automatic numbering, but at least I get `X` columns.

\afterpage{\clearpage%
    \LTXtable{\linewidth}{table.tex}
}


% Sweet sweet automatic numbering, but no lovely `X` columns.

% \afterpage{\clearpage%
%   \begin{ThreePartTable}
%     \begin{TableNotes}
%       \item [a] A note.
%     \end{TableNotes}
%     \begin{longtable}[c]{%
%       @{}%
%       >{\bfseries}l<{}%
%       >{\collectcell\iupac}l<{\endcollectcell}% This is the column with the tabularx `X` column when using ltxtable
%       S%
%       @{}%
%     }
%       \caption{Caption!}\\
%       \multicolumn{2}{@{}l}{\textbf{Molecule}} & {\pKa}\\
%       \endfirsthead
%
%       \insertTableNotes
%       \endlastfoot
%
%       \multicolumn{2}{@{}l}{\emph{Pyridines}}                             \\
%       \fancylabel[CSX]{pyr}      &  pyridine            &  5.23           \\
%       \fancylabel[CSX]{2me-pyr}  &  2-methylpyridine    &  5.97           \\
%       \multicolumn{2}{@{}l}{\emph{Diazines}}                              \\
%       \fancylabel[CSX]{pdz}      &  pyridazine          &  2.24\tnote{a}  \\
%       \multicolumn{2}{@{}l}{\emph{Phenols}}                               \\
%       \fancylabel[CSX]{phe}      &  phenol              &  9.99           \\
%       \fancylabel[CSX]{23me-phe} &  2,3-dimethylphenol  &  10.50          \\
%     \end{longtable}
%   \end{ThreePartTable}
% }

\end{document}

Ideally I'd like to keep the autonumbering of my compounds. There are a few... If I have to remove a feature to get this to work it'll be the X columns. I'll replace the X column with a p{} column. I can determine the width of the p column with a prelininary run through where I include my tables with the \LTXtable{<width>}{<file>} command, get the width from thw .aux file, and then just use an \input command. I'd just rather not have to do this manually for a large document, with potentially many tables.

Aside
I know of the conflict between etoolbox and etextools (and so autonum and fancylabel) and have implemented the fix here. While the MWE doesn't include biblatex my full document does. I've tested the MWE with and without the fix and it makes no difference.