It should be OK to upgrade automatically to the latest version, I do.
You can check your Java version is in Windows with :-
C:\>java -version
java version "1.6.0_11"
Java(TM) SE Runtime Environment (build 1.6.0_11-b03)
Java HotSpot(TM) Client VM (build 11.0-b16, mixed mode, sharing)
If your version is lower than 1.6 upgrade
3ND installs it's own Java but if other applications modify something it could cause problems.
Check the environment variable on your PC. JAVA_HOME if this has been modified it will cause problems.
3Com's Knowledge base has a fuller description of this and can be found in this Solution ID: 3KB23526.
You can get to the knowledge base here:-
http://knowledgebase.3com.com/The Doc