I don't know why (don't have time to find out), but you're printing a backspace.

Before the s///:

length = 14
31 2e 32 33 34 2e 35 36 37 2e 08 2c 38 39
 1  .  2  3  4  .  5  6  7  . ^H  ,  8  9

After the s///:

length = 11
31 32 33 34 35 36 37 08 2c 38 39
 1  2  3  4  5  6  7 ^H  ,  8  9
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Update: It's the \b. \b means backspace in a string literal.

Update: Here's a quickly written solution:

my $num_in = 1234567.89;
my ($i, $d) = split /\./, $num_in;
$i = reverse($i);
$i =~ s/\G(\d{3})(?!$)/$1./g;
$i = reverse($i);
my $num_out = "$i,$d";
print($num_out, "\n");
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