You didn't fully implement my first one.

Same user and same environment!

If it is running as a CGI command, it is being passed a lot of information in %ENV. Try changing the code that has trouble to something like this:

#! /usr/bin/perl
use Data::Dumper;
print "text/plain\n\n";
print Dumper \%ENV;
[download]

That gives you the environment. Do a bunch of export foo=bar to set up that environment and see what happens when you run this offline.

There is a difference between what you are executing and what the webserver does. You need to track that down.