Also another note...I see a bunch of these warnings in the event logs and I wondering if this could one of the reasons the scan could be taking a long time,
Could not scan 221 files inside C:\Program Files\Apache Software Foundation\Tomcat 5.0\webapps\public\WEB-INF\patches\4-0-499\agentPatch.jar due to extraction errors encountered by the Decomposer Engines.
We have a lot .jar files on the server and they are some kind of compressed file so if this the case we have more the 70 compressed files, but I am wondering if it is also able to get into some of the .jar files and this is why it is scanning so many files...
I will try one night without scanning the compressed files and see if the number goes down.