After installing EclEmma 126.96.36.199205091942 as per bug 3522487, running eclemma still did not show results. Rebuilding my eclipse environment from scratch revealed a conflict with JMockit.
JMockit uses a java agent, but provides a non standard means of loading it. Standard means is to specify "-javaagent:jmockit.jar" as a jvm arg. JMockit also allows dynamic loading on jvm > 1.6 using an api provided by the jvm as long as jmockit.jar is before junit.jar in the classpath. It's this dynamic loading that cause EclEmma trouble.
When jmocket is loaded via -javaagent argument, eclemma displays results fine. If jmocket is loaded dynamically, EclEmma 2.1.1 displays results fine, but EclEmma 2.1.2 will not, the test process will not complete, and killing it will cause an error in eclipse.
The error: "'com.mountainminds.eclemma.internal.core.launching.AgentServer' has encountered a problem. Error while dumping coverage data (code 5013)." starts to make sense, seeming to indicate agent issues.