When JAR files in project change you will need to manually update your Eclipse project to reflect these changes. Simply right-click on project, go to properties -> build path and add the new JAR files in. If some JAR files have been removed, you will need to remove those from references also.

For example with new acegi versions you will need to remove version 1.0.2/1.0.3 JARs and add the 1.0.5 JARs instead. SVN will take care of actually adding and deleting the files, you just need to make the Eclipse project aware of the changes.