Are there any error messages in the WLS log or console output to help isolate this problem. Also please provide your environment info (select insert above).
Some initial thoughts:
1) Sounds like your weblogic commandline is different from how you have configured the MyEclipse WLS8 connnector. The 1st place to start if no errors or warnings in the WLS log is to diff the launch strings from the two launch modes. When you launch WLS from ME, view the JDK properties of the Weblogic instance from the Eclipse debug perspective. Just right-click on the top-level WLS application node and select “properties” to view the launch string used by MyEclipse. Compare this string to that generated from commandline. I’m guessing there is a jar file or other commandline option missing in the ME configuration.
2) Are you launching WLS8 with the same JDK from commandline as well as from within ME?