One of MJD's red flags: whenever you've got variables named $fooone and $footwo you probably want an array. Likewise here, you've got multiple arrays named with indicies which means you probably want a hash.

my $cur_section = 0;
my %sections;
while( <TEXTFILE> ) {
  if( /^;section(\d+)/ ) {
    $cur_section = $1;
    next;
  }

  unless( $cur_section ) {
    warn "No section defined for `$_'\n";
    next
  }

  push @{ $sections{ $cur_section } }, $_
}
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