If you increase your debug level to at least 4 Apache::Registry will log the filename passed by the Apache web server and various other information along the way. This may help you identify where the problem is. I don't have mod_perl 1.x available, but it appears you can set debugging level by including the following in your CGI script:

use Apache::Debug level => 4
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Is the problem only with one script or are all your scripts failing?

Have you tried a simple script like the following:

  #!/usr/bin/perl
  print "Content-type: text/plain\n\n";
  print "mod_perl rules!\n";
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Or, for a little more information about your request, you might try the following:

use Apache::Debug ( );
my $r = shift;
Apache::Debug::dump($r, "some comment", "another comment", ...);
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It might also help if you showed a copy of the relevant sections of your web server configuration.