The deployment is done using the following steps.
1) Classloaders are created
2) MBeans are instantiated and registered with the
Sounds like your problem is with step 1
Why can't the MBeanServer in step 2 see your classes that
should have been deployed in step 1?
Can you jar -tf the deployment and any subdeployments?
You can filter irrelevent bits to keep it small.
We're not exactly sure what the problem was. By rebuilding the jar containing the classes that were not being found by the loader, we were able to stop the problem from happening. I'd guess there was something wrong with that jar, but we queried the ServerInfo MBean after the server was up and saw that the class was deployed.
Thanks for the advice; if we see it again, we're probably just going to explode the offending jar into the directory structure. This is really just an issue for a few of us doing infrastructure development. In the end, most will only have jars.