The issue with your posted code can be traced back to your not using Text::CSV to parse the data, which I find ironic given your node title (Update: previous title "Text::CSV"). With your splitting above, your data values are $x = '"001"', not the $x = '001' you seem to expect. If you had turned on warnings, you would have gotten Argument ""2"" isn't numeric in numeric comparison (<=>) repeatedly, since "2" is clearly not numeric. Text::CSV will automatically clean up the quotes, and thus your numbers would have been properly be interpreted as numbers. A la:

#!/usr/bin/perl
use strict;
use warnings;
use Text::CSV;

my $sheet;
my $count = -1;

my $csv = Text::CSV->new ( { binary => 1 } )  # should set binary attr
+ibute.
    or die "Cannot use CSV: ".Text::CSV->error_diag ();

my @rows = ();
while ( my $row = $csv->getline( *DATA ) ) {
    push @rows, $row;
}
my $header = shift @rows;

foreach my $row ( sort { $a->[0] <=> $b->[0] || $a->[1] <=> $b->[1] } 
+@rows ) {
  print join( ',', @$row ), "\n";
}

__DATA__
Name,Score,State
"001","67","CA"
"2","67","CA"
"12","63","FL"
"1","72","IL"
"1","32","AZ"
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See Use strict warnings and diagnostics or die.