I have a related problem. 
There are two ways to configure Websphere for JMX. One is non supported and involves defining and using the platform MBean server. When I use this configuration, I can connect jconsole to the JMX MBean server and I can see the logback JMX information and can call the MBean actions. When I use the supported configuration, it uses a Websphere class of some kind and a JSR160RMI connector and I cannot access the JMX information for logback.

Platform MBean - not supported by IBM, logback JMX is available, only part of the JMX data for Websphere is available.
JSR160RMI - supported by IBM, logback JMX is not available, all of the JMX data for Websphere is available.

I have looked through the code for the JMXConfiguratorAction. It makes the following call:
MBeanServer mbs = ManagementFactory.getPlatformMBeanServer();
Is it possible that getPlatformMBeanServer returns null when Websphere is configured to use the JSR169RMI connector? If so, how would the JMXConfigurator react and where would I expect to see any error messages generated?
Or, is it possible that there are more than one MBeanServer and logback is being registered to a different one than what is being connected to by jconsole or other JMX clients (such as the one included in AppDynamics, which I also use)?