I'm not a huge fan of upgrading software. I have found, in the words of Sam Gamgee's gaffer, that "Short cuts make long delays." In my view you will usually save time troubleshooting by doing a full install rather than an upgrade. Recently we needed to upgrade a customer from Coldfusion 7 to Coldfusion 8. It was a single server installation and we needed a minimum of downtime so, after writing a rollback plan and prepping the server we chose the "upgrade". All seemed to go well. All the data sources, services and settings ported over to the new Coldfusion 8 installation and the server fired up just fine. We thought we were home free until....
We rolled a new application that made use of the Flex Data Services (now called Lifecycle DS ES or something like that). We had been testing the application on a Coldfusion 8 dev server and we were confident that it worked well and that it would tolerate the load. We rolled it live and watched for any hiccups. What we saw was an immediate increase in processor usage and sudden stability issues. Under load the server would simply freeze up. We set up a restart for every 4 hours (about the limit of the uptime) and starting trying to figure out plan B. Back on the test server we verified that the JVM and other tuning settings were the same. After a day of trying this or that our rope came to an end. The only difference we could find was that the dev serve had been installed "from scratch" and the production server had been "upgraded". We bit the bullet and uninstalled Coldfusion 8 and reinstalled it from scratch.
After reinstallation the processors came down to normal levels and memory assumed a normal pattern of behavior - no more hung Jrun. The point here is that a fresh install is often better than an upgrade. A secondary point is that if you are making use of FDS and on CF 8 and you are having trouble, consider whether or not your installation is an upgrade. Cutting to the chase and reinstalling from scratch might do the trick for you if it is.
As for the diagnosis? I can only assume that some remnant of the CF 7 server or some FDS setting that I missed was brought over with the upgrade. If I knew what it was I could possibly diagnose it and fix it without resulting to a reinstall (which is normally a remedy of last resort).