I'm encountering the same issue.
I did discover you have to put the javaagnet parameter prior to the calling out the runnable jar. Doing this got the javaagent to start and to log the following, but still there are no metrics getting sent to our appdynamics servers.
[Thread-0] Mon Jul 18 15:43:06 MDT 2016[INFO]: JavaAgent - Using Java Agent Version [Server Agent v4.2.3.1 GA #12088 raa409c5461baacd62f5f549f6637ffed0530fcdd 49-4.2.3.next-build]
[Thread-0] Mon Jul 18 15:43:06 MDT 2016[INFO]: JavaAgent - Running IBM Java Agent [No]
[Thread-0] Mon Jul 18 15:43:06 MDT 2016[INFO]: JavaAgent - Java Agent Directory [D:\agent\ver4.2.3.1]
[Thread-0] Mon Jul 18 15:43:06 MDT 2016[INFO]: JavaAgent - Java Agent AppAgent directory [D:\agent\ver4.2.3.1]
[Thread-0] Mon Jul 18 15:43:06 MDT 2016[INFO]: JavaAgent - ####################################################################################
[Thread-0] Mon Jul 18 15:43:06 MDT 2016[INFO]: JavaAgent - Java Agent Directory [D:\agent\ver4.2.3.1]
[Thread-0] Mon Jul 18 15:43:06 MDT 2016[INFO]: JavaAgent - Java Agent AppAgent directory [D:\agent\ver4.2.3.1]
[Thread-0] Mon Jul 18 15:43:06 MDT 2016[INFO]: JavaAgent - Using Java Agent Version [Server Agent v4.2.3.1 GA #12088 raa409c5461baacd62f5f549f6637ffed0530fcdd 49-4.2.3.next-build]
[Thread-0] Mon Jul 18 15:43:06 MDT 2016[INFO]: JavaAgent - All agent classes have been pre-loaded
[Thread-0] Mon Jul 18 15:43:06 MDT 2016[DEBUG]: JavaAgent - Using Java Version [JAVA_18] for AppDynamics Java Agent
Running obfuscated agent
Started AppDynamics Java Agent Successfully.
[Thread-0] Mon Jul 18 15:43:08 MDT 2016[INFO]: JavaAgent - Started AppDynamics Java Agent Successfully.
I believe somehow for springboot to work with the appdyamics javaagent, the javaagent has to be embedded in the springboot jar during build time so it can listen on the embeded tomcat instance that spring boot launches.
