We tried McAfee PortalShield and had the same problem (installing it out-of-the-box broke file uploading). That was enough to scare us off. We are now using Sybari Antigen for Sharepoint. It seems to be a decent piece of software  (and the only other tried-and-true application for sharepoint  Portal Server 2003 antivirus on the market). It installed  easily and I think the user interface is intuitive. All the configuration options I was looking for are there (email notifications, effective logging, ability to set up periodic antivirus definition updates, etc.)