Interesting. Using your code in another script in the same directory. I'm getting the following. Not sure where that gets me but results I did not expect.

==> /var/log/apache2/error.log <==
Directory is /srv/site/scripts
Contents are 
total 36
drwxr-xr-x  2 derek derek  4096 Feb  4 17:49 .
drwxrwxr-x 10 derek derek  4096 Feb  4 17:04 ..
-rw-------  1 derek derek 12288 Feb  4 17:49 .test3.pl.swp
-rw-r--r--  1 derek derek     7 Feb  4 17:09 config.txt
-rw-r--r--  1 derek derek   434 Feb  4 17:41 test.pl
-rw-r--r--  1 derek derek   394 Feb  4 17:41 test2.pl
-rw-r--r--  1 derek derek   118 Feb  4 17:49 test3.pl
[download]

As far as Apache goes the config is just simply:

<Files ~ "\.(pl|cgi)$">
    SetHandler perl-script
    PerlResponseHandler ModPerl::PerlRun
    Options +ExecCGI
    PerlSendHeader On
</Files>
[download]

Quick update and curious as to the difference.

The header of the file on the old server is: #!/usr/local/bin/perl

The scripts that we've been testing with are: #!/usr/bin/perl

And the one provided in your test script was: #!/usr/bin/env perl

When we update the scripts in questions to use the #!/usr/bin/env perl they seem to work.

Thanks for your help been a long time since I've done perl and coming back at this as a noob.