Hi, i am experiencing the same problem:

httpd.conf

        <Perl>
         
        </Perl>
        PerlSetEnv TESTENV "asdf"
          <Perl>
        warn Data::Dumper::Dumper(\%ENV);
        </Perl>

Output:

root@joakim-laptop:/etc/apache2# service apache2 start
 * Starting web server apache2                                                  
                                                                               
$VAR1 = {
          'TESTENV' => 'asdf',
          'PATH' => 
'/usr/local/bin:/usr/bin:/bin:/home/db2inst1/sqllib/bin:/home/db2inst1/sqllib/adm:/home/db2inst1/sqllib/misc:/home/db2inst1/sqllib/db2tss/bin',
          'MOD_PERL_API_VERSION' => 2,
          'MOD_PERL' => 'mod_perl/2.0.5'
        };

httpd.conf
        PerlSetEnv TESTENV "asdf"
          <Perl>
        warn Data::Dumper::Dumper(\%ENV);
        </Perl>

Output:
root@joakim-laptop:/etc/apache2# service apache2 start
 * Starting web server apache2                                                  
                                                                               
$VAR1 = {
          'PATH' => 
'/usr/local/bin:/usr/bin:/bin:/home/db2inst1/sqllib/bin:/home/db2inst1/sqllib/adm:/home/db2inst1/sqllib/misc:/home/db2inst1/sqllib/db2tss/bin',
          'MOD_PERL_API_VERSION' => 2,
          'MOD_PERL' => 'mod_perl/2.0.5'
        };
 

My configuration:
root@joakim-laptop:/etc/apache2# cat /etc/lsb-release 
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=11.10
DISTRIB_CODENAME=oneiric
DISTRIB_DESCRIPTION="Ubuntu 11.10"
root@joakim-laptop:/etc/apache2# dpkg --get-selections | grep apache
apache2                                         install
apache2-mpm-worker                              install
apache2-threaded-dev                            install
apache2-utils                                   install
apache2.2-bin                                   install
apache2.2-common                                install
libapache2-mod-apreq2                           install
libapache2-mod-perl2                            install
libapache2-mod-perl2-dev                        install
libapache2-reload-perl                          install
libapache2-request-perl                         install
root@joakim-laptop:/etc/apache2# dpkg -s libapache2-mod-perl2
Package: libapache2-mod-perl2
Status: install ok installed
Priority: optional
Section: httpd
Installed-Size: 3736
Maintainer: Ubuntu Developers <ubuntu-devel-disc...@lists.ubuntu.com>
Architecture: i386
Version: 2.0.5-2ubuntu1
Depends: perl (>= 5.12.3-6ubuntu4), perlapi-5.12.3, libapr1 (>= 1.2.7), 
libaprutil1 (>= 1.2.7+dfsg), libc6 (>= 2.4), libperl5.12 (>= 5.12.3), apache2 | 
apache2-mpm-itk, apache2.2-common, libdevel-symdump-perl, liburi-perl, 
libwww-perl, netbase
Recommends: libbsd-resource-perl, libapache2-reload-perl
Conffiles:
 /etc/apache2/mods-available/perl.load 19ba69a03d3e3d23ac13407c2ad7bdbb
Description: Integration of perl with the Apache2 web server
 mod_perl allows the use of Perl for just about anything
 Apache-related, including <Perl> sections in the config
 files and the famous Apache::Registry module for caching
 compiled scripts.
 .
 It can produce anywhere from a 400% to 2000% speed increase
 on sites using perl scripts, and is used on many large script-
 based web sites - for example, http://slashdot.org.
Homepage: http://perl.apache.org/
Original-Maintainer: Debian Perl Group 
<pkg-perl-maintain...@lists.alioth.debian.org>
root@joakim-laptop:/etc/apache2# dpkg -s libapache2-mod-perl2-dev
Package: libapache2-mod-perl2-dev
Status: install ok installed
Priority: optional
Section: libdevel
Installed-Size: 352
Maintainer: Ubuntu Developers <ubuntu-devel-disc...@lists.ubuntu.com>
Architecture: all
Source: libapache2-mod-perl2
Version: 2.0.5-2ubuntu1
Depends: libapache2-mod-perl2 (>= 2.0.5-2ubuntu1), libapache2-mod-perl2 (<< 
2.0.5-2ubuntu1.1~)
Description: Integration of perl with the Apache2 web server - development files
 mod_perl allows the use of Perl for just about anything
 Apache-related, including <Perl> sections in the config
 files and the famous Apache::Registry module for caching
 compiled scripts.
 .
 This package contains the header files required for building
 C-based modules integrating with mod_perl.
Homepage: http://perl.apache.org/
Original-Maintainer: Debian Perl Group 
<pkg-perl-maintain...@lists.alioth.debian.org>
root@joakim-laptop:/etc/apache2#

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https://bugs.launchpad.net/bugs/305646

Title:
  PerlSetEnv not working consistently in libapache2-mod-perl

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