I suspect that the text you want to replace contains '\n' characters. I have created the following code to inspect your code -

#!/usr/local/bin/perl -w
use strict;

my $pagecode;
{
  local $/;
  $pagecode = <DATA>;
}

my $content = "Roger";

print "before:\n---------\n$pagecode\n";

# fix 1
$pagecode =~ s/<!--BeginContent-->(?:.|\n)*<!--EndContent-->/<!--Begin
+Content-->$content<!--EndContent-->/;

# fix 2
$pagecode =~ s/<!--BeginPages-->.*<!--EndPages-->/<!--BeginPages--><!-
+-EndPages-->/s;

print "after:\n---------\n$pagecode\n";

__DATA__
<!--BeginContent-->Hello World!
This is a comment line
<!--EndContent-->
<!--BeginPages-->Hello World!
<!--EndPages-->
[download]

Note that there are many ways to fix this problem. By the way, you can drop the capture ( .. ) in your regexp too.

The first method - replace (.*) in your regexp with (?:.|\n)*.

The second method - add the 's' switch at the end of the regexp.