That ought to be working except that if you are using dataElement the startTag/endTag pairs are redundant and will generate pairs of nested tags.

The sample code below works for me and is essentially what you are trying to do:

use strict;
use warnings;
use XML::Writer;

my $writer = new XML::Writer();

$writer->xmlDecl();
$writer->startTag("Main");
$writer->startTag("NewHits");
$writer->dataElement( "GI" , "Element string");
$writer->endTag("NewHits");

$writer->endTag("Main");
$writer->end();
[download]

<?xml version="1.0"?>
<Main><NewHits><GI><GI>Element string</GI></GI></NewHits></Main>
[download]

Note: reducing your sample code to a small example that demonstrates the problem will not only get a better response from the monks, but may reveal your problem along the way.