This works as expected (it keeps the comments):

use warnings;
use strict;
use XML::Twig;

my $str = <<EOF;
<foo>

    <!-- hello comment -->

    <bar>goo</bar>

</foo> 
EOF

my $t = XML::Twig->new(comments => 'keep');
$t->parse($str);
$t->print();
print "\n";

__END__

<foo>

    <!-- hello comment -->

    <bar>goo</bar></foo>
[download]

Try to create a small example like this that anyone can run which still demonstrates the problem.