mmartin68 ,
Sorry that you are seeing this issue with MyEclipse.
Can you answer some more questions for us to understand the issue better ?
1) Can you please share your Build ID from Help > About MyEclipse Blue Edition > Build ID ?
2) Which version of RAD are you migrating your projects from ?
3) Also share the version of WAS server you are working with.
4) Can you please send us all the files in the .settings folder of this project ? Also please send us the .project and .classpath files to help us with our investigation. You can mail them to support@genuitec.com ATTN Swapna with a link to this thread.