When creating a JUnitStories class, the overridden configuration method is no longer executed starting in JBehave 3.9.2.
I also tested this with 3.9.3, 3.9.5 and 4.0-beta-11 and the issue persists. Only by changing the dependency version in my POM back to 3.9.1 does the method override correctly again.
I have attached my StoryReporter class, the abstract class where the issue presents when version >= 3.9.2 and an example Embeddable JUnitRunner class that inherits from it.
MyStoryReporter.class is simply a Reporter that prints information to System.out where every callback prints a line starting with [JBEHAVE] and emits whatever information is available:
You can run any story file from resources and see that the StoryReporter does not get used unless you are on a version prior to 3.9.2. You can also add a breakpoint in configuration and see that the breakpoint will be hit in 3.9.1 but is never hit in 3.9.2 and later.