A quick update to (hopefully) help anyone else looking at this problem.

Having done a bit of quick maths I decided that the problem was, if I want to retain the padding, that the code was allocating too much space to the sub-cats. Therefore, I edited the files category_row.php and new_products.php and amended the calculation of the width from

$col_width = floor(100/$num_categories);

to
$col_width = floor(90/$num_categories);

This seems to have had the desired effect.

cheers
Guy