Aslak, thanks for creating JIRA issue.
Currently 2 open issues in Glassfish:
https://glassfish.dev.java.net/issues/show_bug.cgi?id=13016 <-- workaround in DeployableContainer impl
New GlassFish embedded integration should work with v. 3.0.1-b04 up til and including 3.1-b09. Any version above 3.1-b09 will fail due to 13017.
Also note that GlassFish 3.1 now has a REST interface to the admin console. At some point I'd like to get a container implementation that uses this interface. I spoke with Jason Lee and he may be able to lend a hand in the implementation.