In my case, I have many archives that get deployed (up to 9 in one test case). I noticed that my tests we are all working over JMX, but since we consider them integration tests I wanted to run them closer to how they should run so I switched over to servlet 3.0 protocol (and yes I included the protocol in my path). In addition, my deployments are created using ShrinkWrap's maven resolver to pull them down. I don't recreate them instead I just import the created archive as a java archive (everything is essentially an EJB JAR).
I found that many tests failed, and after researching it was because JBoss AS 7 was looking in test.war!/WEB-INF/ for jboss-deployment-structure.xml not one of the files in the lib directory, which is exactly as designed. However Arquillian doesn't seem to have a way to tell it to use the jboss-deployment-structure.xml from my JAR as the WAR file.
I could change the deployment to create a WAR but that impacts my resulting structure since we look explicitly for JARs based on where they should be tested.