You need to reset $count for each file.    Something like this (UNTESTED): 

#!/usr/bin/perl
use strict;
use warnings;

$^I = ".bak"; 
undef $/;

my $count = 0;

while ( my $line = <> ) {
    $line =~ s{
        (<\/div>)
        }  {
        ++$count == 2
            ? "\t<?php include(\$_SERVER['DOCUMENT_ROOT'].\"\/includes
+\/footer.php\"); ?>\n\n$1"
            : $1
        }gex;
    print $line;
    $count = 0;
    }

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In reply to Re: How to process multiple input files? by jwkrahn
in thread How to process multiple input files? by rnaeye

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