You should probably be using Bio::SeqIO from the BioPerl package. I was able to extract the sequence from your sample GenBank file.

#!/usr/bin/perl
use strict;
use warnings;
use Bio::SeqIO;

my $in  = Bio::SeqIO->new( -file   => "sample_gb.gb" ,
                           -format => 'GenBank');
my $out = Bio::SeqIO->new( -file   => '>fasta.dat',
                           -format => 'fasta');

while ( my $seq = $in->next_seq() ) {
    $out->write_seq($seq);
}
[download]

Contents of 'fasta.dat' were:

>NC_004905 Influenza A virus (A/Hong Kong/1073/99(H9N2)), complete gen
+ome.
AGCAGGGTTAATAATCACTCACTGAGTGACATCAACATCATGGCGTCGCAAGGCACCAAA
CGATCCTATGAACAGATGGAAACTGGTGGAGAACGCCAGAATGCCACTGAGATCAGGGCA
TCTGTTGGAAGAATGGTTGGTGGAATTGGGAGGTTTTACGTACAGATGTGCACTGAACTC
AAACTCAGCGACCAAGAAGGAAGGTTGATCCAGAACAGTATAACAATAGAGAGAATGGTT
CTCTCCGCATTTGATGAAAGGAGGAACAGGTACCTAGAGGAACATCCCAGTGCGGGGAAG
GACCCGAAGAAGACCGGAGGTCCAATCTACCGAAGGAGAGACGGGAAATGGGTGAGAGAG
CTGATTCTGTATGACAAAGAGGAGATAAGGAGAATTTGGCGTCAAGCGAACAATGGAGAA
GACGCAACTGCTGGTCTCACTCATATGATGATCTGGCATTCCAACCTAAATGATGCCACA
TACCAGAGAACAAGAGCCCTCGTGCGGACTGGAATGGACCCCAGAATGTGCTCTCTGATG
CAAGGATCAACCCTCCCGAGGAGATCTGGAGCTGCTGGTGCAGCAATAAAGGGAGTCGGG
ACAATGGTAATGGAACTAATTCGGATGATAAAGCGAGGCATTAATGACCGGAACTTCTGG
AGAGGCGATAATGGACGAAGAACAAGGATTGCATATGAGAGAATGTGCAACATCCTCAAA
GGGAAATTTCAAACAGCAGCACAAAGAGCAATGATGGATCAGGTGCGAGAAAGCAGAAAT
CCTGGGAATGCTGAAATTGAAGATCTCATCTTTCTGGCACGGTCTGCACTCATCCTGAGA
GGATCCGTAGCCCATAAGTCCTGCTTGCCTGCTTGTGTGTACGGGCTCGCTGTGGCCAGT
GGATATGATTTTGAGAGGGAAGGGTACTCTCTGGTTGGGATAGATCCTTTCCGTCTGCTT
CAGAACAGTCAGGTCTTCAGTCTTATTAGACCAAATGAGAATCCAGCACATAAAAGTCAA
TTGGTATGGATGGCATGCCATTCTGCAGCATTTGAGGACCTGAGAGTCTCAAGTTTCATT
AGAGGAACAAGAGTGATCCCAAGAGGACAACTATCCACTAGAGGAGTTCAGATTGCTTCA
AATGAGAACGTGGAAGCAATGGATTCCAGCACTCTTGAACTGAGAAGCAGATATTGGGCT
ATAAGGACCAGGAGTGGAGGAAACACCAATCAACAGAGAGCATCTGCAGGACAAATCAGT
GTACAGCCCACTTTCTCAGTACAGAGAAATCTTCCCTTCGAAAGACCGACCATTATGGCT
GCGTTTAAGGGGAATACCGAGGGCAGAACATCTGACATGAGGACTGAAATCATAAGGATG
ATGGAAAGTGCCAGACCAGAAGATGTGTCTTTCCAGGGGCGGGGAGTCTTCGAGCTCTCG
GACGAAAAGGCAACGAACCCGATCGTGCCTTCCTTTGACATGAGTAATGAAGGATCTTAT
TTCTTCGGAGACAATGCAGAGGAATATGACAATTGAGGAAAAATACCCTTGTTTCTA
[download]