I know you didn't ask, but some of the code used here is not very secure. Other parts can be written better (if you plan to make the script portable)

Here is an updated version:

#!/usr/bin/perl
use strict;         # amen
use warnings 'all'; # or use perl -w
use File::Basename;

$| = 1;

# :raw for brain-dead OSes (or use binmode).
open my $in, '<:raw', $ARGV[0];        # use $in not IN
open my $out, '>:raw', "differences";

while (<$in>) {
    chomp;
    ($file,$problem,@machines) = split(/,/, $_);

    ($name,$path,$suffix) = fileparse($file,"");
    print "$name -- $path -- $suffix\n";

    if($problem eq "different") {
        # get the file from the remote machine
        foreach $machine (@machines) {
            next if ($machine eq "");

            # consider using File::Temp here
            $tempfile = "/tmp/" . $name . "_" . $machine;

            # should consider using File::Remote here
            system("rcp", "$machine:$file", $tempfile) == 0
                or die "Execution (rcp) failed: $?";

            # why not use Text::Diff ?
            print "comparing $name from $machine\n";
            system("diff", $file, $tempfile) == 0
                or die "Execution (diff) failed: $?";

            print "(k)eep or (i)gnore this difference?\n";
            $resp = <STDIN>;
            print ">>$resp<<\n";
            if($resp eq "k") {
                print $out "$machine $file\n";
            }
        }
    }
}
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Executing stuff is always insecure. You should either consider using taint mode (-T) or use Perl modules to perform the same task in most cases (in all cases in the example above)

Documents for these modules are here: File::Remote, File::Temp and Text::Diff. They are more or less simple to use, a lot safer and sometimes faster. (since they don't fork() and exec())

Update: Use chomp instead of chop.