You have this posted in the wrong section for Hiajckthis analysis. You need to post it in the correct location. However, since this is a potentially infected server, your best option is to reformat. Out removal team can only remove known infections, and the fact that you feel your server is infected is a strong argument for there being an infection that will not be detected. Servers are a favorite target for rootkits.
Additionally, if your anti-virus is finding tracking cookies, then you have been using your server to surf the web, which is a huge no-no. My suggestion, from someone who has run their own server for a few years now, reformat, lock down the box, and leave it as a server.
If you still want to get help, go here:http://www.bleepingcomputer.com/forums/t/34773/preparation-guide-for-use-before-using-malware-removal-tools-and-requesting-help/