The example given below gives me a strange offset in 4th decimal place in the parenthesis. Interestingly, this problem arose only after I updated my Miktex 2.8 to Miktex 2.9. I don't know whats causing this is slight shift in the last decimal point in the second row.

Here is the code for above output.
\documentclass[12pt]{article}
\usepackage{amsfonts}
\usepackage{amsmath,array}
\usepackage[detect-all]{siunitx}
\usepackage[margin=1 in]{geometry}
\usepackage{booktabs, longtable}
\usepackage[english]{babel}
\begin{document}
\begin{table}[htbp]
\footnotesize
\centering
\sisetup{input-symbols=(), table-figures-integer = 3, table-figures-decimal = 4, table-number-alignment = center}
\begin{tabular}{lSSSSSS}
\toprule
& {\bf (A)} & {\bf (B)} & {\bf (C)} & {\bf (D)} & {\bf (E)} & {\bf (F)} \\
\hline \midrule
& 0.0016*** & 0.0013*** & 0.0015*** & 0.0015*** & 0.0009** & 0.0009** \\
& (0.0005) & (0.0005) & (0.0006) & (0.0006) & (0.0004) & (0.0005) \\
& & & & 0.1324*** & 0.1202*** & 0.1203*** \\
& & & & (0.0131) & (0.0118) & (0.0118) \\
& & & & -0.0549*** & -0.0569*** & -0.0569*** \\
& & & & (0.0023) & (0.0024) & (0.0024) \\
\hline \bottomrule
\end{tabular}
\end{table}
\end{document}



group-digits=false(I believegroup-decimal-digits=falseis now deprecated but still works) to the\ssisetupshould fix it. – Peter Grill Mar 28 '12 at 22:49{}). I took the liberty to format you post a little. See this link for more details on available formatting. – Peter Grill Mar 28 '12 at 22:50group-digits=falseb) an answer. :-) – lockstep Mar 28 '12 at 22:53