Here is my MWE. As you can see, the problem only happens when we use the macro \suppOrApp.
\documentclass{article}
\usepackage[english]{babel}
\usepackage{blindtext}
\usepackage{caption}
\usepackage{float}
\usepackage{ifthen}
\title{A caption test}
\author{Some one}
\date{\today}
\begin{document}
\newcommand{\suppOrApp}{
\ifthenelse{\boolean{thesisStyle}}
{Appendix}
{Supplementary}
}
\newboolean{thesisStyle}
\setboolean{thesisStyle}{false} % Might want to reconsider this here.
% This has additional space:
\renewcommand{\tablename}{\textbf{\suppOrApp Table}}
% But this would work fine.
%\renewcommand{\tablename}{\textbf{Supporting Table}}
\begin{table}
\begin{tabular}{cc}
1 & 2 \\
3 & 4 \\
\end{tabular}
\caption{\blindtext}
\label{mytable}
\end{table}
\blindtext
Please refer to Supporting Table~\ref{mytable}.
\end{document}
%here:\newcommand{\suppOrApp}{%– Werner Apr 09 '14 at 22:49%) at the end of lines? – Werner Apr 09 '14 at 22:50