Mario,
Sorry that you are seeing this issue.
Can you answer some more questions for us ?
1. Can you please copy paste the Installation Details from MyEclipse > Installation Summary > Installation Details ?
2. Which version of WAS are you working with ?
3. Is your project a WTP project ? If yes then I recommend recreating the project using MyEclipse Web Project wizard. MyEclipse 11 will have comprehensive support for WTP projects.
4. If the build is the only issue you are seeing with this project, then you can edit org.eclipse.wst.common.project.facet.core.xml file and remove <runtime> element.
Let us know how it works for you.