\documentclass[journal]{IEEEtran}

\usepackage{graphicx}

\usepackage{subfig}

\usepackage{lipsum}

\usepackage{afterpage}

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\makeatletter

\newcommand{\setcaptype}[1]{\def\@captype{#1}}

\makeatother

​

\newsavebox{\tempbox}

​

\begin{document}

​

\savebox{\tempbox}{\begin{minipage}{\textwidth}% measuer height of figure

\setcaptype{figure}%

\centering

    \subfloat[]{\includegraphics[width=0.4\linewidth]{example-image-a}}

    \hfill

    \subfloat[]{\includegraphics[width=0.4\linewidth]{example-image-b}}

    \caption{Some dummy figures.}

    \label{fig1}

\end{minipage}}

​

\begin{figure}[t]

\rlap{\usebox\tempbox}

\end{figure}

\afterpage{\begin{figure}[t]% next column

\rule{0pt}{\dimexpr \ht\tempbox+\dp\tempbox}

\end{figure}}

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\section{This text should follow Fig. \ref{fig1}, not precede it!}

\lipsum[1-6]

​

% Problem happens also after a \clearpage

\clearpage

\savebox{\tempbox}{\begin{minipage}{\textwidth}% measuer height of figure

\setcaptype{figure}%

\centering

    \subfloat[]{\includegraphics[width=0.8\linewidth,height=0.2\textheight]{example-image-c}}

    \caption{Another figure.}

    \label{fig2}

\end{minipage}}

​

\begin{figure}[t]

\rlap{\usebox\tempbox}

\end{figure}

\afterpage{\begin{figure}[t]% next column

\rule{0pt}{\dimexpr \ht\tempbox+\dp\tempbox}

\end{figure}}

​

\section{This text should follow Fig. \ref{fig2}, not precede it!}

\lipsum[1-6]

​

\end{document}