I have set up a FileAudit filter but all logs are showing the user as NT AUTHORITY\SYSTEM. I installed the hotfix suggested in this post: Re: file audit nt authority but it hasn't worked?
Please update to 6.1 and let the LEM upgrade the Agents. Some operations will always show SYSTEM but you should see user names for most delete, create and write events once you upgrade.
What version of LEM are you using? Is NT Authority\System the only user that appears in FIM logs?
LEM version is 6.0 I think. NT Authority\System is the only user showing under the File Audit filters (including the one that is pre-setup)