I managed to solve my problems with the axgen build stuff.

the log4j.properties file does really need to be in a directory on the classpath. (Though it sure seemed like occasionaly the current directory can end up on the classpath without specifying it)

This solved my first problem with log4j not being initialized propertly.

The netbeans mdr reader will create a directory called etc/ and store a few files in this directory. If for some reason those files are corrupted the mdr reader won't be able to initialize itself. Removing the directory will cause those files to be regenerated correctly. (It would've been nice if the error message was more helpful).

This fixed my second problem.