Firstly, running the following works fine on my machine (on a recent active state perl install), and produces output as you describe.

my $xml = "<tbody>one\ttwo\tthree</tbody>\n"x40;

$xml =~ s#<tbody>((?:[^<]+|<(?!/?tbody>))+</tbody>(?:\s*<tbody>(?:[^<]
++|<(?!/?tbody>))+</tbody>)*)#"<tbody>\n".${TableBody(\$1)}."\n</tbody
+>"#gies;
print $xml;

sub TableBody
{
    my ($line) = @_;
    $temp = "$$line";
    $temp =~s#</tbody>$##;
    $temp =~s#\t#</para></entry><entry><para>#g;
    $temp ="<row><entry><para>$temp</para></entry></row>";

    $temp =~s#<tbody>#<row><entry><para>#g;
    $temp =~s#</tbody>#</para></entry></row>#g;
    return \$temp;
}
[download]

Secondly, If you're going to give an example, it's nice to give a working example so that people can easily reproduce your error.

Thirdly, your code seems a bit obfusacted. Without knowing what you're trying to do it's hard to give advice, but I'd suggest a starting point as something like the following, which produces the same results as your script.

my $xml = "<tbody>one\ttwo\tthree</tbody>\n"x5;
$xml =~ s#<tbody>(.*?)</tbody>#${TableBody(\$1)}#gies;
print $xml;

sub TableBody
{
    my $line_ref = shift;
    my $return_xml;

    foreach my $thing (split(/\t/, $$line_ref)) {
        $return_xml .= "<entry><para>$thing</para></entry>";
    }
    return \"<row>$return_xml</row>";
}
[download]

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