Anti-virus software should be running on all machines in a properly-managed network including servers even if other threat prevention measures are in place. It should run on servers as well as workstations for two reasons:
- They're the most critical computers in your environment, much more than client systems, and
- 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 is plenty of malware which can automatically spread across your network if it can get hold even of a single host.
Most problems are generally more related to properly configuring your anti-virus software.
AV and Malware products need to be designed for server installations, not workstation based AV/Malware installed in a server environment.
There's no software you can "just install and run" without thinking twice about what you're doing.