An extra tidbit: HTML::Table is a red herring.

my $new_elt = XML::Twig::Elt->new('div');
$new_elt->set_inner_html('');
$new_elt->paste(before => $_);
[download]

is enough to trigger the problem, but the following isn't

my $new_elt = XML::Twig::Elt->new('div');
#$new_elt->set_inner_html('');
$new_elt->paste(before => $_);
[download]