The code that you posted appears to work fine on Windows 2000 with Activestate 5.6.1.

If you are losing carriage returns, check that they have not been chomped from string contained in $regel.

If you are generating HTML then you will need to change the substitution to add the <br> tag e.g.
$regel =~ s/Username/<br>\nGebruikersnaam/sgm;

#! /usr/bin/perl -w

use strict;
use warnings;

undef $/;
my $regel = <DATA>;
$regel =~ s/Username/\nGebruikersnaam/sgm;
print "start\n";
print "$regel";
print "end\n";
__DATA__
Username=Joe Smith
Username=Jane Doe

Gives you:

start

Gebruikersnaam=Joe Smith

Gebruikersnaam=Jane Doe
end

Inman
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