I looked at some of the code to process the logs and noticed some of the perl modules you use. I checked my server and found that many were missing! I don't remember perl modules being listed under the install requirements. The clean Fedora Core 4 install does not install many of the modules you use. I grepped through the files and installed the ones that you use. I hope I did not miss anything. Do you have a list of all the modules a Zimbra install requires?
Now.... What are the implications of the missing modules on the zimbra install? I went ahead and did the GA upgrade again since I noticed you used some perl scripts during the install/upgrade.
The raw_logs are now showing entries for messages sent/received. No errors in zmlogger.out even with a stop/start. No changes in the graphs.... yet.
Edited: Well, that is silly.. I just figured out that Zimbra supplies the modules.