Did you try it with perl 5.10 or newer?

Yes, as1000/v5.10. As you can see below, the 14000 (last) run is aborted after 16 minutes elapsed and 15+ minutes of cpu. I'll leave it running while I sleep and see what happens.

#! perl -slw
use strict;
use constant {
    CHROM => 'chromosome.txt',
    PROBES => 'probes.txt',
};

our $N ||= 1000;

my $chrom;
open C, '<', CHROM or die CHROM . ": $!";
sysread C, $chrom, -s( CHROM ) or die $!;
close C;
$chrom = uc $chrom;

open P, '<', PROBES or die $!;
my @probes = <P>;
close P;
chomp @probes;

warn "Trying $N probes with perl $]";

warn time;
my $re = join '|', @probes[ 0 .. $N ];
$re = qr[($re)];

print "$1 : $-[ 0 ]" while $chrom =~ m[$re]g;

warn time;

__END__
[13:47:01.65]C:\test>\Perl510\bin\perl5.10.0.exe -s 668954.p10 -N=1000
+ > nul
Trying 1000 probes with perl 5.010000 at 668954.p10 line 21.
1203515291 at 668954.p10 line 23.
1203515295 at 668954.p10 line 29.

[13:48:16.15]C:\test>\Perl510\bin\perl5.10.0.exe -s 668954.p10 -N=1200
+0 > nul
Trying 12000 probes with perl 5.010000 at 668954.p10 line 21.
1203515310 at 668954.p10 line 23.
1203515335 at 668954.p10 line 29.

[13:50:56.37]C:\test>\Perl510\bin\perl5.10.0.exe -s 668954.p10 -N=1300
+0 > nul
Trying 13000 probes with perl 5.010000 at 668954.p10 line 21.
1203515469 at 668954.p10 line 23.
1203515494 at 668954.p10 line 29.

[13:51:35.67]C:\test>\Perl510\bin\perl5.10.0.exe -s 668954.p10 -N=1400
+0 > nul
Trying 14000 probes with perl 5.010000 at 668954.p10 line 21.
1203515696 at 668954.p10 line 23.
Terminating on signal SIGINT(2)  ### Over 15 minutes of CPU used by th
+is point

[14:08:03.32]C:\test>
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