I would be very surprised if this script caused your issue. What kind of output do you see if you run the following in a TTY context: 
#!/usr/bin/perl

use strict;
use warnings;

my @files = </home/user/Maildir/cur/*>;
for (@files){
    open(IN, $_);
    while (<IN>) {
        last if /The mail system/;
    }
    while (<IN>) {
        if (m#/domain.com$#) {
            print "\n";
            last;
        }
        print;
    }
    close IN;
}

[download]
There are a number of methodological changes I'd make to what you've done, particularly adding a check to see if what you are about to open is a file (-f or next; and see -f) and testing the result of the open (open(IN, '<', $_) or die "Open failure on $_:$!\n"), but these shouldn't be the cause of your issue unless you've got an unbelievably large set of subdirectories and have swamped your log file. Which you said you didn't.

#11929 First ask yourself `How would I do this without a computer?' Then have the computer do it the same way.

In reply to Re: Runaway CGI script by kennethk
in thread Runaway CGI script by Pascal666

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