msariman,
Can you please recheck the mappings in the Deployment Assembly (right click on project> Properties > MyEclipse > Deployment Assembly ) with respect to the libraries?
If you are still seeing issues,
1. please attach a screenshot of the Deployment Assembly page.
2. Which deployment mode are you using (Classic,Enhanced,In-Workspace mode) ?
3. Also let us know the details about the project and on which version of MyEclipse was it created.