It is not uncommon for malware to have self protection measures in place to prevent removal. Such tricks as blocking access to security websites, killing beneficial security tool processes/services, and preventing Windows Updates from running are quite widespread today. They are definitely signs of infection but they are not unique to Conficker.
Take a look at the following Eye Chart
If you fall into category 2 or 3 (those in red) please read http://spywarehammer.com/simplemachinesforum/index.php?topic=88.0
, so we can determine what type of infection you have and help you remove it.