Which free antivius is best Comodo Antivirus and ClamWin AV

Yes, although for the most part they are configured to scan for viruses overnight with real-time file protection disabled, the exceptions are:

• File servers - Set to scan on write only. Full nightly scan.
• Sharepoint - No current anti-virus, waiting on Sophos for SharePoint to come out of beta.
• Exchange - Exchange specific anti-virus soloution. Overnight scans exclude data stores.
• Application Servers - SQL Data stores excluded from overnight scans.
• AD/DC/DHCP - Overnight scan set to exclude service specific data files and logs

Anti-virus software should definitely be running on all machines in a properly-managed network, even if other threat prevention measures are in place. It should run on servers too, for two reasons: 1) they're the most critical computers in your environment, much more than client systems, and 2) they're no less at risk only because nobody actively uses (or at least should not being actively using) them for surfing the web: there's plenty of malware which can automatically spread across your network if it can get hold even of a single host.

That said, your problem is more related to properly configuring your anti-virus software.

The product you're using comes with built-in firewalling: that's something that should be taken into account when running it on server systems, and configured accordingly (or turned off at all).

Some years ago, anti-virus software was (in)famous for randomly deleting Exchange databases if by chance it came across a viral signature inside some e-mail message stored in the physical data file; every anti-virus vendor warned about this in the product manual, but some people still failed to grasp it and got their stores nuked.

There's no software you can "just install and run" without thinking twice about what you're doing.