# Issues centering table with altered fontsize

I am doing my thesis and want to have all table consistently centered on the page, and \footnotesize text. For some reason one table decides to left justify when I make it footnote size (or any other size):

\begin{table}[H]
\caption{Variants in genes with AF $< 0.01$ in Individual II1, Family A.}
\label{table:BBS_var}
\begin{footnotesize}
\centering
\begin{tabular}{llllrr}
\hline
\textbf{Gene} & \textbf{Nucleotide} & \textbf{Amino-acid} & \textbf{Transcript} &  \textbf{ESP} & \textbf{GERP}\\
&   \textbf{change} & \textbf{change} & \textbf{ID} & \textbf{AF} &\textbf{++} \\
\hline
\textit{Lorem}  & . & . & Lorem  & 0.00186 & 5.4  \\
\textit{Lorem} & . & . & Lorem            & .        & 2.25 \\
\textit{Lorem}  & .  & . & Lorem          & .        & 5.67 \\
\textit{Lorem}  & .  & . & Lorem             & 0.000116 & 5.67 \\
\hline
\end{tabular}
\end{footnotesize}
\end{table}

If I remove the \footnotsize lines then it centres the table fine, but is the wrong size text obviously.

I can also use \begin{centre} within the table environment, but then this adds a large gap between the caption and table, which is also undesired.

I have another almost identical table (aside from the data) which reduces size without issue. I have tried copying this table and repopulating it for the data for this table, but then the issue magically manifests again.

Any ideas? It's starting to make me feel I'm going a little bit insane now....

PS. Using Pdflatex 2013.9.11, preamble is:

%% General layout
\documentclass[12pt,a4paper,oneside]{book}
\usepackage{fullpage}
\usepackage{tikz}
\usepackage{microtype}
\usepackage[onehalfspacing]{setspace}
\usepackage[bindingoffset=2cm,margin=2cm]{geometry}
\usepackage[utf8]{inputenc} % UTF8 encoding solves issuse in references with obscure characters
\usepackage[british]{babel}
\usepackage{csquotes}
\usepackage{amsmath}
\usepackage[toc,page]{appendix}
\usepackage{pdfpages}
\usepackage{listings}
\usepackage{color}
\usepackage{subfigure}
%Figure layout
\usepackage{graphicx}
\usepackage{float}
\usepackage[margin=12pt,font=footnotesize,labelfont=bf,labelsep=colon]{caption}
\graphicspath{{./figures/}}

%PDF bookmarks
\usepackage{bookmark}

\usepackage{fancyhdr}
\pagestyle{fancy}
• try putting the \centering outside the footnotesize environment. – Steven B. Segletes Mar 29 '14 at 19:53
• Cheers, his has fixed the problem for this table. I'm very confused as to why this wasn't a problem for the other table though, oh well. – Reuben John Pengelly Mar 29 '14 at 20:26