I added a Security Domain (manually) to my JBoss application. It included a definition of a custom login module as well as a reference to the module in which it was contained:

<login-module code="com.atlassian.crowd.application.jaas.CrowdLoginModule" flag="required" module="com.atlassian.crowd">

Through multiple startups and shutdowns my configuration worked as I expected.
When I attempted to use the Admin Console to add new module options to this security domain, my ability to login failed.
Upon further investigation I discovered that the admin console removed the module property from the login-module tag.

to prove this I repeated the process with the same result.