I copied your code and ran it against the data you provided and it works the way you would expect on my computer. I'm not sure what's going on here, but here's the code (I added newlines to your print statements):

#!/usr/bin/perl
use strict;
use warnings;

my $file = "sizes";

open(my $fh, '<', $file) or die "Could not open '$file' $!\n";

while (my $line = <$fh>)
{
    chomp $line;
    my ($drive, $sizegb, $freegb) = split (/,/,$line);

    print qq($sizegb\n);
    $sizegb /= 1024;
    print qq($sizegb\n);
}
[download]

For the data in file "sizes", I used what you provided, minus the headers. Here's the output:

95342874624
93108276
2119757824
2070076
3295703040
3218460
[download]