I noticed an ugly problem with our classpath implementation this week while working on my Android application (Fireside Talk - a native client for Campfire). I moved some code into a lib-project and added a JAR library there. As a result my main project couldn't see classes from this JAR although the dependency was correctly processed. The project was built but the IDE support (editor, navigation) was affected. This is fixed now and you will see plugin update notification soon.
Please be patient. There is some problems with our autoupdate center hosted on kenai.com. Requests for plugin catalog are redirected and IDE is not processing them correctly. I will look for some solution and post an update soon.