Am not sure what you mean. How do you override LogManager? And even if the LogManager is overridden, then shouldn't the jboss-classloading.xml file be indicating to the ClassLoader to use the one from the war and nothing from outside the war?
At boot time we override the JDK's LogManager with our own.
But I'm just guessing, as I'm pretty sure the classloading is setup as you define it -- with deployers picking up jboss-classloading.xml.
Hence the issue must be somewhere else.