What kind of Java application is that? Is it running in the same JVM instance as the one you launched with those system properties? How exactly are you starting the server and which exact version of AS7/WildFly is this?
You can use "ps" to print the command line arguments used to start JBoss AS - look at all of the java processes, one of them will be it. Verify that the -D values you set in standalone.conf are set. (By the way, I assume you are not running Windows...)