I'm running tomcat 5.54 on FreeBSD with java 1.4.2 and I'm running in a strange situation. When I add a new xml file to $Catalina_home/conf/Catalina/localhost to create a new context using the autoload feature, the xml file disappears when I shutdown/startup the server.
From the docs: "When using automatic deployment, the docBase defined by an XML Context file should be outside of the appBase directory. If this is not the case difficulties may be experienced deploying the web application or the application may be deployed twice."
Also, have you got a WAR file version of the app in appBase? it might be getting deployed twice and one of them overwrites the XML file?
you're also on the bleeding edge with 5.5.x and 5.5.6 is the most recent release in that line: I'd try upgrading if you want to stick with 5.5. Otherwise, try 5.0.30, and don't let the beta scare you (since the alpha didn't).