First of all, read this :
http://www.cgisecurity.net/articles/xss-faq.shtml

Then if you findout that the webserver itself is vulnerable to XSS, which i doubt. 
You might have found a CGI hosted on the server vulnerable to XSS, in any case once 
you find out for sure, then see if that website/CGI is responsible for issuing cookies 
or for the Authentication of cookies.
If it is not, then your XSS alert is going to be an alert only in your Final Report, 
and you could say that the bad-coding or non-security conscious coding practices have 
been exercised during coding of CGI's.


Regards
--------
Muhammad Faisal Rauf Danka

Head of GemSEC / Chief Technology Officer
Gem Internet Services (Pvt) Ltd.
web: www.gem.net.pk
Key Id: 0x784B0202
Key Fingerprint: 6F8C EDCF 6C6E 06A5 48D7  6A20 C592 484B 
784B 0202

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