When the server gets in this state, it happens for all non-mod_perl CGIs. I also made the simplest CGI I could think of for testing, which also fails:

#!C:/Perl/bin/perl

use strict;

print "Status: 200 OK

Test";
[download]

If I then put this same script under mod_perl, it works fine. I will do what you said and report back with any findings or non-findings.

I am getting the sense that the script isn't being executed at all.