Apache resp. mod_perl is wrapping your CGI script in a subroutine to repeatedly call it.
This is the right explanation, but maybe the meaning is not completely clear. When you use Apache::Registry to run your script, it literally adds a set of brackets around your script and makes the whole thing into a sub, kind of like this: 
sub handler {
   #!/usr/bin/perl
   use strict;
   use warnings;
   use CGI;
   my $cgi = new CGI;
   print_document_header();
   sub print_document_header {
      print $cgi->header( -type => 'text/html' ), "\n";
   }
}

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Your workaround of explicitly passing around the variable is a good one in my opinion.
I completely agree, but if you're allergic to good programming practice you can just use our $cgi instead of my $cgi.

In reply to Re^2: Variable will not stay shared in a sporadically crashing CGI by Anonymous Monk
in thread Variable will not stay shared in a sporadically crashing CGI by Locutus

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