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.