I tried your code on my machine, with a few additions/modifications to get it running, all of them marked with "# **" below. I didn't see any problem with the output. The only really significant modifications were to take the "my" away from the "$c" in the while loop, since it was re-initializing $c with each pass through the loop, and to add binmode(IN), which actually doesn't make any difference with the data I'm using.

Try this modified code on your machine and see if you get appropriate output. It only processes the first two numbers, so it should be easy to see what's going on and play with it.

use warnings;                   # **
use strict;                     # **

my $data;                       # **
my $c = 0;                      # **
my $outfile = 'tempo.pk';       # **
my $infile = shift;             # **

open(IN,  " < $infile" );
binmode(IN);                    # ** prevents newline translation
my $si=2;   # the number of entries is known
my %matrix;
while($c<$si) {                 # ** removed my
    read(IN, my $bin, 4);
    $data = unpack('N', $bin);  

    my $d = Unshuffle($c);

    print "$c -> $d ($data)\n";  # **
    $matrix{$d} += $data/3;      # **

    $c++;
}
close( IN );
open(OUT, " >$outfile" );
foreach my $d (sort {$a <=> $b} (keys %matrix)) {
    print "$outfile $d ($matrix{$d})\n"; # **
    print (OUT pack('V', $matrix{$d}));
}
close( OUT );

open(IN, " <$outfile" );         # **
while( read(IN, my $bin, 4) ) {  # **
   $data = unpack('V', $bin);    # **
   print "$data:";               # **
}                                # **


sub Unshuffle { # ** interchange the first two positions
   my $val = shift;
   return 1   if ($val == 0);
   return 0   if ($val == 1);
   return $val;
}
# output was
#  0 -> 1 (2140)
#  1 -> 0 (1544028160)
#  tempo.pk 0 (514676053.333333)
#  tempo.pk 1 (713.333333333333)
#  514676053:713:
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