Dear Fahad ,
I am not sure if your Problem is resolved Or you still need help however we faced a similar situation at customer end last year and as per my engineers , MSRT ( Microsoft Malicious Software Removal tool) was working better as compared to any other Antivirus Software .Try that on your DC and few clients .
There is also another software named Combofix ( download from Bleepingcomputer.org) which is very useful however try it on one of the clients first .
Also download conficker detection tool from the URL mentioned below and scan your network .It will tell you how many machines are infected .For each machine ,do the following .
a) Remove network cable and Run MSRT or Combofix
b) Restart the machine .Apply Windows Patch .Restart again and than Scan the whole machine with SAV .
c) Once completely scanned and found clean ,connect the network cable back .
http://www.foundstone.com/us/resources-free-tools.asp
Hopefully it should help . Remember that it copies itself to USB Drives as well so you need to scan and clean all the USB Memory sticks Or hard disks which are being used in your company .