I did raise a question about this on StackOverflow, and eventually also created a patch to fix the issue.
The problem occurs in Websphere, as myfaces is always on the classpath. When setting classloading to PARENT_LAST, Mojarra is correctly initialised with the jar that I bundle in the war, but RF4 incorrectly decides to use the ResourceTrackerForMyfaces.
Please check for more information and my patch:
After applying it, my application ran faultlessly with Mojarra