So It looks like I need to understand why the HTTP header is different when accessing an HTML page than it would be accessing a Perl page.

I would next try a network sniffer (wireshark works for me) to inspect the HTTP traffic between the browser and web server. If the cookie is complete in the HTTP traffic, then you have an issue in your web server. If not, then you have an issue in your browser.

Thank you for that Advice - I turned the problem over to my network group and found our netscaler is stripping cookies. I should no better than to blame it on Perl!