I remember running through the sample repository on a previous version of EAM, but it appears to be incompatible with EAM v3.

Is there another sample for v3, or is that something that the project team is working on?

I have been unable to find documentation on the scripting and Python; the only reference I can see indicates that the meta-model is exposed through 'kb', but I haven't been able to find anything else. Is there a tutorial or description of the Python classes that are available?

I'm having similar symptoms, though clearly it's a different problem. I'm NOT using Apache, it's straight-to-Tomcat6. I installed the patches you posted above, and I still get an error on the Protege-side telling me to look at memory problems on the server. The file reportXML.xml in web_apps appears...