MH12,
Sorry that you are seeing this issue.
Can you give us some more details to help investigate the issue further ?
1. Please copy paste the Installation Details from MyEclipse > Installation Summary > Installation Details ?
2. Did you create the project internally in MyEclipse or imported from elsewhere ? If its imported from elsewhere, did you enhance the project to work with MyEclipse ?
3. Please copy paste the entire stacktrace of the error you are seeing. Also clear the contents of the .log file which is located at <workspace dir>/.metadata/.log, replicate the issue and copy paste the contents of the .log file here for us.
4. Please share the steps in detail right from project creation till adding deployment to WAS 6.1 to help us replicate the issue at our end.