eclipse 188.8.131.52 has an annoying bug. Try to import a WAR file that contains class files in WEB-INF/classes. Thes class files are not imported into the right folder in the imported project structure.
Importing a WAR file gets you a special folder ImportedClasses which is supposed to contain the package/folder structure for imported classes. Due to a bug in the eclipse WAR importer they are copied to ImportedClasses/WEB-INF/classes. As a result, starting a deployed web application presents plenty of ClassNotFoundExceptions and the like.
Today I tried this again with eclipse 3.4-M4 and was glad to see this bug fixed, I was already preparing to file a bug. Until 3.4 is released the classes must be moved manually to the right folder!