Bad Antivirus

Dear folks,

I have 3 W2K3 servers, each are running same software binary exe files. One month ago, they infected with some rootkits and viruses which later on I know from antivirus detection this malware called sality, ipz, etc.
After installing a new antivirus and revealed the malware, some of my software seems not running as expected. At the moment, I suspect that the malware still there because the AV may not capable to clean them all. I tried using 3 or 4 most popular AV, but all were claimed the servers are clean while my software couldn't run smoothly. In fact, some of exe files has been changed in size while I am not sure whether this changed made by viruses or 'bad' AV I just installed.
If I try to proof that my exe files has been changed by this 'bad' AV, does anyone know how to proof this things ? By reversing this exe files, is it possible to get which part of the files has changed ?

Thank's

Ibha ID
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