Removing history doesn't always work!
I'm having the same kind of problem: upon startup AS 7.1.0.Final removes a segment I added to standalone-full.xml. More specifically, the <jms-connection-factories> definition inside the <subsystem xmlns="urn:jboss:domain:messaging:1.1"> definition is yanked out.
I tried (in order):
1) Deleting contents under the standalone_xml_history directory.
2) Deleting the standalone_xml_history directory.
3) Deleting contents under the standalone-full_xml_history directory.
4) Deleting the standalone-full_xml_history directory.
And no success. AS 7.1 is still silently "doctoring" my standalone-full.xml. Interesting thing is that the connection factory I define in the section that is removed works. But then, if I bounce the server it won't be there anymore.