While working with a customer recently the subject of file level antivirus came up. There is an update to the article for 2007 that discusses those exclusions. Please take a moment to ensure that your environment is indeed excluding those directories. It's simple to check but very hard to diagnose a random behavior or deadlock that may be caused by the lack of proper exclusions.
The article can be found here:
952167 Certain folders may have to be excluded from antivirus scanning when you use a file-level antivirus program in SharePoint