Sounds like the tests you are running are executing the jar file and not running off of the source code. Make sure that in Run Configurations, under the test you are running, the classpath tab has the jme3 project listed under the user entries. Also make sure it is the actual source code of the test case you are running, and not the compiled test in the jar file.
Whenever a program is running and it does not reflect the code, it means it is running in a different location. You have to Refresh in eclipse a lot, and sometimes execute Project->clean